Session Info## [8] base
##
## other attached packages:
-## [1] patchwork_1.2.0 ggplot2_3.5.1 forcats_1.0.0 tidyHeatmap_1.10.3
+## [1] patchwork_1.2.0 ggplot2_3.5.1 forcats_1.0.0 tidyHeatmap_1.10.2
## [5] tidyr_1.3.1 dplyr_1.1.4
##
## loaded via a namespace (and not attached):
## [1] viridis_0.6.5 sass_0.4.9 utf8_1.2.4
-## [4] generics_0.1.3 shape_1.4.6.1 digest_0.6.36
+## [4] generics_0.1.3 shape_1.4.6.1 digest_0.6.37
## [7] magrittr_2.0.3 RColorBrewer_1.1-3 evaluate_0.24.0
## [10] iterators_1.0.14 circlize_0.4.16 fastmap_1.2.0
## [13] foreach_1.5.2 doParallel_1.0.17 jsonlite_1.8.8
@@ -794,10 +795,10 @@ Session Info## [49] ragg_1.3.2 dendextend_1.17.1 pkgconfig_2.0.3
## [52] desc_1.4.3 gtable_0.3.5 pkgdown_2.1.0
## [55] pillar_1.9.0 bslib_0.8.0 glue_1.7.0
-## [58] systemfonts_1.1.0 highr_0.11 xfun_0.46
+## [58] systemfonts_1.1.0 highr_0.11 xfun_0.47
## [61] tibble_3.2.1 tidyselect_1.2.1 knitr_1.48
-## [64] farver_2.1.2 rjson_0.2.21 htmltools_0.5.8.1
-## [67] labeling_0.4.3 rmarkdown_2.27 compiler_4.4.1
+## [64] farver_2.1.2 rjson_0.2.22 htmltools_0.5.8.1
+## [67] labeling_0.4.3 rmarkdown_2.28 compiler_4.4.1
diff --git a/authors.html b/authors.html
index 3e72b11..a4f8c52 100644
--- a/authors.html
+++ b/authors.html
@@ -17,7 +17,7 @@
diff --git a/index.html b/index.html
index 8041696..daec21a 100644
--- a/index.html
+++ b/index.html
@@ -33,7 +33,7 @@
diff --git a/pkgdown.yml b/pkgdown.yml
index 363b499..7f032c4 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,4 +3,4 @@ pkgdown: 2.1.0
pkgdown_sha: ~
articles:
introduction: introduction.html
-last_built: 2024-08-05T07:04Z
+last_built: 2024-09-03T06:56Z
diff --git a/reference/N52.html b/reference/N52.html
index bcc502d..d649855 100644
--- a/reference/N52.html
+++ b/reference/N52.html
@@ -17,7 +17,7 @@
@@ -67,6 +67,16 @@ Example data set N52
Format
An object of class tbl_df (inherits from tbl, data.frame) with 520 rows and 15 columns.
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
@@ -71,6 +71,10 @@ add_annotation
)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -111,6 +115,12 @@ Value
Details
To be added.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
diff --git a/reference/add_bar-method.html b/reference/add_bar-method.html
index 0a6dec9..e14466f 100644
--- a/reference/add_bar-method.html
+++ b/reference/add_bar-method.html
@@ -18,7 +18,7 @@
@@ -70,6 +70,10 @@ DEPRECATED. Adds a bar annotation layer to a `InputHeatmap`, that on evaluat
add_bar(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -107,6 +111,12 @@ Details
![[Maturing]](figures/lifecycle-maturing.svg)
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/add_class.html b/reference/add_class.html
index b24d545..a12ec5b 100644
--- a/reference/add_class.html
+++ b/reference/add_class.html
@@ -17,7 +17,7 @@
diff --git a/reference/add_line-method.html b/reference/add_line-method.html
index a57e591..0af9f5b 100644
--- a/reference/add_line-method.html
+++ b/reference/add_line-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ DEPRECATED. Adds a line annotation layer to a `InputHeatmap`, that on evalua
add_line(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/add_point-method.html b/reference/add_point-method.html
index c046259..11b5d4c 100644
--- a/reference/add_point-method.html
+++ b/reference/add_point-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ DEPRECATED. Adds a point annotation layer to a `InputHeatmap`, that on evalu
add_point(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/add_tile-method.html b/reference/add_tile-method.html
index 7a3c633..3a3453b 100644
--- a/reference/add_tile-method.html
+++ b/reference/add_tile-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ DEPRECATED. Adds a tile annotation layer to a `InputHeatmap`, that on evalua
add_tile(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/annot_to_list.html b/reference/annot_to_list.html
index 5df2c5b..da9afef 100644
--- a/reference/annot_to_list.html
+++ b/reference/annot_to_list.html
@@ -17,7 +17,7 @@
diff --git a/reference/annotation_bar-method.html b/reference/annotation_bar-method.html
index c9a5f23..a5aa7e6 100644
--- a/reference/annotation_bar-method.html
+++ b/reference/annotation_bar-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a bar annotation layer to a `InputHeatmap`, that on evaluation creates
annotation_bar(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/annotation_line-method.html b/reference/annotation_line-method.html
index 4d6db8c..cc6ab1d 100644
--- a/reference/annotation_line-method.html
+++ b/reference/annotation_line-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a line annotation layer to a `InputHeatmap`, that on evaluation creates
annotation_line(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/annotation_point-method.html b/reference/annotation_point-method.html
index 39a3631..64c06ef 100644
--- a/reference/annotation_point-method.html
+++ b/reference/annotation_point-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a point annotation layer to a `InputHeatmap`, that on evaluation create
annotation_point(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/annotation_tile-method.html b/reference/annotation_tile-method.html
index a82469f..426e717 100644
--- a/reference/annotation_tile-method.html
+++ b/reference/annotation_tile-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a tile annotation layer to a `InputHeatmap`, that on evaluation creates
annotation_tile(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/as_ComplexHeatmap-method.html b/reference/as_ComplexHeatmap-method.html
index 575f030..dc31276 100644
--- a/reference/as_ComplexHeatmap-method.html
+++ b/reference/as_ComplexHeatmap-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,11 @@ Creates a `ComplexHeatmap` object for less standard plot manipulation (e.g.
as_ComplexHeatmap(tidyHeatmap)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -82,6 +87,15 @@ Value
Details
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/as_matrix.html b/reference/as_matrix.html
index f8c2c67..78251a2 100644
--- a/reference/as_matrix.html
+++ b/reference/as_matrix.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_counts_is_na.html b/reference/check_if_counts_is_na.html
index 78ffc42..0c30be2 100644
--- a/reference/check_if_counts_is_na.html
+++ b/reference/check_if_counts_is_na.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_duplicated_genes.html b/reference/check_if_duplicated_genes.html
index 866689e..3b976e8 100644
--- a/reference/check_if_duplicated_genes.html
+++ b/reference/check_if_duplicated_genes.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_wrong_input.html b/reference/check_if_wrong_input.html
index 8993332..5a2697d 100644
--- a/reference/check_if_wrong_input.html
+++ b/reference/check_if_wrong_input.html
@@ -17,7 +17,7 @@
diff --git a/reference/drop_class.html b/reference/drop_class.html
index 52cfec2..2172cfc 100644
--- a/reference/drop_class.html
+++ b/reference/drop_class.html
@@ -17,7 +17,7 @@
diff --git a/reference/error_if_log_transformed.html b/reference/error_if_log_transformed.html
index ee6fbc1..defd568 100644
--- a/reference/error_if_log_transformed.html
+++ b/reference/error_if_log_transformed.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_abundance_norm_if_exists.html b/reference/get_abundance_norm_if_exists.html
index e7a2174..edd351c 100644
--- a/reference/get_abundance_norm_if_exists.html
+++ b/reference/get_abundance_norm_if_exists.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements.html b/reference/get_elements.html
index e3b1670..60cf049 100644
--- a/reference/get_elements.html
+++ b/reference/get_elements.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements_features.html b/reference/get_elements_features.html
index 3455ee1..e9692b2 100644
--- a/reference/get_elements_features.html
+++ b/reference/get_elements_features.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements_features_abundance.html b/reference/get_elements_features_abundance.html
index 70c577e..39673e1 100644
--- a/reference/get_elements_features_abundance.html
+++ b/reference/get_elements_features_abundance.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_counts.html b/reference/get_sample_counts.html
index e84e325..4f757d9 100644
--- a/reference/get_sample_counts.html
+++ b/reference/get_sample_counts.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_transcript.html b/reference/get_sample_transcript.html
index 1fcba07..c195cd5 100644
--- a/reference/get_sample_transcript.html
+++ b/reference/get_sample_transcript.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_transcript_counts.html b/reference/get_sample_transcript_counts.html
index 47f42db..095bd16 100644
--- a/reference/get_sample_transcript_counts.html
+++ b/reference/get_sample_transcript_counts.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_x_y_annotation_columns.html b/reference/get_x_y_annotation_columns.html
index b26bbd8..746ba88 100644
--- a/reference/get_x_y_annotation_columns.html
+++ b/reference/get_x_y_annotation_columns.html
@@ -17,7 +17,7 @@
diff --git a/reference/heatmap-method.html b/reference/heatmap-method.html
index 18c355d..b5fb9a4 100644
--- a/reference/heatmap-method.html
+++ b/reference/heatmap-method.html
@@ -17,7 +17,7 @@
@@ -115,6 +115,10 @@ Creates a `InputHeatmap` object from `tbl_df` on evaluation creates a `Compl
)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -171,6 +175,12 @@ Details
This function takes a tbl as an input and creates a `ComplexHeatmap` plot. The information is stored in a `InputHeatmap` object that is updated along the pipe statement, for example adding annotation layers.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/ifelse2_pipe.html b/reference/ifelse2_pipe.html
index 14b24ad..3af0be6 100644
--- a/reference/ifelse2_pipe.html
+++ b/reference/ifelse2_pipe.html
@@ -17,7 +17,7 @@
diff --git a/reference/ifelse_pipe.html b/reference/ifelse_pipe.html
index cc63a57..f67868e 100644
--- a/reference/ifelse_pipe.html
+++ b/reference/ifelse_pipe.html
@@ -17,7 +17,7 @@
diff --git a/reference/index.html b/reference/index.html
index fe03263..82f5113 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
diff --git a/reference/input_heatmap.html b/reference/input_heatmap.html
index 9e00831..c2050e8 100644
--- a/reference/input_heatmap.html
+++ b/reference/input_heatmap.html
@@ -17,7 +17,7 @@
@@ -73,6 +73,10 @@ input_heatmap
)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -121,6 +125,12 @@ Value
Details
To be added.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_arrow_down(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_arrow_up-method.html b/reference/layer_arrow_up-method.html
index ec48ffb..a2c1c16 100644
--- a/reference/layer_arrow_up-method.html
+++ b/reference/layer_arrow_up-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_arrow_up(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_asterisk-method.html b/reference/layer_asterisk-method.html
index 4969843..77d5973 100644
--- a/reference/layer_asterisk-method.html
+++ b/reference/layer_asterisk-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_asterisk(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_diamond-method.html b/reference/layer_diamond-method.html
index 30bb1dd..fedbb88 100644
--- a/reference/layer_diamond-method.html
+++ b/reference/layer_diamond-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_diamond(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_point-method.html b/reference/layer_point-method.html
index 9989c4c..9ce3514 100644
--- a/reference/layer_point-method.html
+++ b/reference/layer_point-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_point(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_square-method.html b/reference/layer_square-method.html
index 246c7c6..bca96f3 100644
--- a/reference/layer_square-method.html
+++ b/reference/layer_square-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_square(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_star-method.html b/reference/layer_star-method.html
index c6b7ace..08093fc 100644
--- a/reference/layer_star-method.html
+++ b/reference/layer_star-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_star(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_text-method.html b/reference/layer_text-method.html
index 7270b34..93e478b 100644
--- a/reference/layer_text-method.html
+++ b/reference/layer_text-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of texts above the heatmap tiles to a `InputHeatmap`, that on
layer_text(.data, ..., .value, .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -96,6 +100,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/parse_formula.html b/reference/parse_formula.html
index 5ae7f62..62286c5 100644
--- a/reference/parse_formula.html
+++ b/reference/parse_formula.html
@@ -17,7 +17,7 @@
diff --git a/reference/pasilla.html b/reference/pasilla.html
index 1061f28..7d80340 100644
--- a/reference/pasilla.html
+++ b/reference/pasilla.html
@@ -17,7 +17,7 @@
@@ -67,6 +67,16 @@ Example data set Pasilla
Format
An object of class tbl_df (inherits from tbl, data.frame) with 504 rows and 8 columns.
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
diff --git a/reference/quo_names.html b/reference/quo_names.html
index 49306e9..5143582 100644
--- a/reference/quo_names.html
+++ b/reference/quo_names.html
@@ -17,7 +17,7 @@
diff --git a/reference/save_pdf-Heatmap-method.html b/reference/save_pdf-Heatmap-method.html
index 0a7fdea..76b8374 100644
--- a/reference/save_pdf-Heatmap-method.html
+++ b/reference/save_pdf-Heatmap-method.html
@@ -17,7 +17,7 @@
diff --git a/reference/save_pdf-InputHeatmap-method.html b/reference/save_pdf-InputHeatmap-method.html
index ced5637..8cbe274 100644
--- a/reference/save_pdf-InputHeatmap-method.html
+++ b/reference/save_pdf-InputHeatmap-method.html
@@ -17,7 +17,7 @@
diff --git a/reference/save_pdf-methods.html b/reference/save_pdf-methods.html
index 5fcb03f..885d04b 100644
--- a/reference/save_pdf-methods.html
+++ b/reference/save_pdf-methods.html
@@ -17,7 +17,7 @@
@@ -69,6 +69,10 @@ Save plot on PDF file
)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -102,6 +106,12 @@ Details
It simply save an `Heatmap` to a PDF file use pdf() function in the back end
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/scale_design.html b/reference/scale_design.html
index 38e2ec2..23bc01d 100644
--- a/reference/scale_design.html
+++ b/reference/scale_design.html
@@ -17,7 +17,7 @@
diff --git a/reference/scale_robust.html b/reference/scale_robust.html
index 8c63e14..d69d4f7 100644
--- a/reference/scale_robust.html
+++ b/reference/scale_robust.html
@@ -17,7 +17,7 @@
@@ -63,6 +63,10 @@ Scale counts in a robust way against sd == 0
scale_robust(y)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -75,6 +79,12 @@ Arguments
Value
A scaled and centred numerical array
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
diff --git a/reference/split-methods.html b/reference/split-methods.html
index d8a3fd1..9bbeba3 100644
--- a/reference/split-methods.html
+++ b/reference/split-methods.html
@@ -18,7 +18,7 @@
@@ -73,6 +73,11 @@ Split the heatmap row-wise depending on the biggest branches in the cladogra
split_columns(.data, number_of_groups)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -99,6 +104,15 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/wrap_heatmap-method.html b/reference/wrap_heatmap-method.html
index 07b1d36..da670bd 100644
--- a/reference/wrap_heatmap-method.html
+++ b/reference/wrap_heatmap-method.html
@@ -23,7 +23,7 @@
@@ -92,6 +92,10 @@ Wrap tidyHeatmap (ComplexHeatmap) in a patchwork-compliant patch
)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -120,6 +124,12 @@ Value
A wrapped_patch object
A wrapped_patch object
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
@@ -133,7 +143,6 @@ Examples
) |>
wrap_heatmap()
-
Example data set N52
Format
An object of class tbl_df (inherits from tbl, data.frame) with 520 rows and 15 columns.
Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+add_annotation
) +Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -111,6 +115,12 @@Value
Details
To be added.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+DEPRECATED. Adds a bar annotation layer to a `InputHeatmap`, that on evaluat
add_bar(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -107,6 +111,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/add_class.html b/reference/add_class.html
index b24d545..a12ec5b 100644
--- a/reference/add_class.html
+++ b/reference/add_class.html
@@ -17,7 +17,7 @@
diff --git a/reference/add_line-method.html b/reference/add_line-method.html
index a57e591..0af9f5b 100644
--- a/reference/add_line-method.html
+++ b/reference/add_line-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ DEPRECATED. Adds a line annotation layer to a `InputHeatmap`, that on evalua
add_line(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/add_point-method.html b/reference/add_point-method.html
index c046259..11b5d4c 100644
--- a/reference/add_point-method.html
+++ b/reference/add_point-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ DEPRECATED. Adds a point annotation layer to a `InputHeatmap`, that on evalu
add_point(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/add_tile-method.html b/reference/add_tile-method.html
index 7a3c633..3a3453b 100644
--- a/reference/add_tile-method.html
+++ b/reference/add_tile-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ DEPRECATED. Adds a tile annotation layer to a `InputHeatmap`, that on evalua
add_tile(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/annot_to_list.html b/reference/annot_to_list.html
index 5df2c5b..da9afef 100644
--- a/reference/annot_to_list.html
+++ b/reference/annot_to_list.html
@@ -17,7 +17,7 @@
diff --git a/reference/annotation_bar-method.html b/reference/annotation_bar-method.html
index c9a5f23..a5aa7e6 100644
--- a/reference/annotation_bar-method.html
+++ b/reference/annotation_bar-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a bar annotation layer to a `InputHeatmap`, that on evaluation creates
annotation_bar(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/annotation_line-method.html b/reference/annotation_line-method.html
index 4d6db8c..cc6ab1d 100644
--- a/reference/annotation_line-method.html
+++ b/reference/annotation_line-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a line annotation layer to a `InputHeatmap`, that on evaluation creates
annotation_line(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/annotation_point-method.html b/reference/annotation_point-method.html
index 39a3631..64c06ef 100644
--- a/reference/annotation_point-method.html
+++ b/reference/annotation_point-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a point annotation layer to a `InputHeatmap`, that on evaluation create
annotation_point(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/annotation_tile-method.html b/reference/annotation_tile-method.html
index a82469f..426e717 100644
--- a/reference/annotation_tile-method.html
+++ b/reference/annotation_tile-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a tile annotation layer to a `InputHeatmap`, that on evaluation creates
annotation_tile(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/as_ComplexHeatmap-method.html b/reference/as_ComplexHeatmap-method.html
index 575f030..dc31276 100644
--- a/reference/as_ComplexHeatmap-method.html
+++ b/reference/as_ComplexHeatmap-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,11 @@ Creates a `ComplexHeatmap` object for less standard plot manipulation (e.g.
as_ComplexHeatmap(tidyHeatmap)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -82,6 +87,15 @@ Value
Details
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/as_matrix.html b/reference/as_matrix.html
index f8c2c67..78251a2 100644
--- a/reference/as_matrix.html
+++ b/reference/as_matrix.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_counts_is_na.html b/reference/check_if_counts_is_na.html
index 78ffc42..0c30be2 100644
--- a/reference/check_if_counts_is_na.html
+++ b/reference/check_if_counts_is_na.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_duplicated_genes.html b/reference/check_if_duplicated_genes.html
index 866689e..3b976e8 100644
--- a/reference/check_if_duplicated_genes.html
+++ b/reference/check_if_duplicated_genes.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_wrong_input.html b/reference/check_if_wrong_input.html
index 8993332..5a2697d 100644
--- a/reference/check_if_wrong_input.html
+++ b/reference/check_if_wrong_input.html
@@ -17,7 +17,7 @@
diff --git a/reference/drop_class.html b/reference/drop_class.html
index 52cfec2..2172cfc 100644
--- a/reference/drop_class.html
+++ b/reference/drop_class.html
@@ -17,7 +17,7 @@
diff --git a/reference/error_if_log_transformed.html b/reference/error_if_log_transformed.html
index ee6fbc1..defd568 100644
--- a/reference/error_if_log_transformed.html
+++ b/reference/error_if_log_transformed.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_abundance_norm_if_exists.html b/reference/get_abundance_norm_if_exists.html
index e7a2174..edd351c 100644
--- a/reference/get_abundance_norm_if_exists.html
+++ b/reference/get_abundance_norm_if_exists.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements.html b/reference/get_elements.html
index e3b1670..60cf049 100644
--- a/reference/get_elements.html
+++ b/reference/get_elements.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements_features.html b/reference/get_elements_features.html
index 3455ee1..e9692b2 100644
--- a/reference/get_elements_features.html
+++ b/reference/get_elements_features.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements_features_abundance.html b/reference/get_elements_features_abundance.html
index 70c577e..39673e1 100644
--- a/reference/get_elements_features_abundance.html
+++ b/reference/get_elements_features_abundance.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_counts.html b/reference/get_sample_counts.html
index e84e325..4f757d9 100644
--- a/reference/get_sample_counts.html
+++ b/reference/get_sample_counts.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_transcript.html b/reference/get_sample_transcript.html
index 1fcba07..c195cd5 100644
--- a/reference/get_sample_transcript.html
+++ b/reference/get_sample_transcript.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_transcript_counts.html b/reference/get_sample_transcript_counts.html
index 47f42db..095bd16 100644
--- a/reference/get_sample_transcript_counts.html
+++ b/reference/get_sample_transcript_counts.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_x_y_annotation_columns.html b/reference/get_x_y_annotation_columns.html
index b26bbd8..746ba88 100644
--- a/reference/get_x_y_annotation_columns.html
+++ b/reference/get_x_y_annotation_columns.html
@@ -17,7 +17,7 @@
diff --git a/reference/heatmap-method.html b/reference/heatmap-method.html
index 18c355d..b5fb9a4 100644
--- a/reference/heatmap-method.html
+++ b/reference/heatmap-method.html
@@ -17,7 +17,7 @@
@@ -115,6 +115,10 @@ Creates a `InputHeatmap` object from `tbl_df` on evaluation creates a `Compl
)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -171,6 +175,12 @@ Details
This function takes a tbl as an input and creates a `ComplexHeatmap` plot. The information is stored in a `InputHeatmap` object that is updated along the pipe statement, for example adding annotation layers.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/ifelse2_pipe.html b/reference/ifelse2_pipe.html
index 14b24ad..3af0be6 100644
--- a/reference/ifelse2_pipe.html
+++ b/reference/ifelse2_pipe.html
@@ -17,7 +17,7 @@
diff --git a/reference/ifelse_pipe.html b/reference/ifelse_pipe.html
index cc63a57..f67868e 100644
--- a/reference/ifelse_pipe.html
+++ b/reference/ifelse_pipe.html
@@ -17,7 +17,7 @@
diff --git a/reference/index.html b/reference/index.html
index fe03263..82f5113 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
diff --git a/reference/input_heatmap.html b/reference/input_heatmap.html
index 9e00831..c2050e8 100644
--- a/reference/input_heatmap.html
+++ b/reference/input_heatmap.html
@@ -17,7 +17,7 @@
@@ -73,6 +73,10 @@ input_heatmap
)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -121,6 +125,12 @@ Value
Details
To be added.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_arrow_down(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_arrow_up-method.html b/reference/layer_arrow_up-method.html
index ec48ffb..a2c1c16 100644
--- a/reference/layer_arrow_up-method.html
+++ b/reference/layer_arrow_up-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_arrow_up(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_asterisk-method.html b/reference/layer_asterisk-method.html
index 4969843..77d5973 100644
--- a/reference/layer_asterisk-method.html
+++ b/reference/layer_asterisk-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_asterisk(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_diamond-method.html b/reference/layer_diamond-method.html
index 30bb1dd..fedbb88 100644
--- a/reference/layer_diamond-method.html
+++ b/reference/layer_diamond-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_diamond(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_point-method.html b/reference/layer_point-method.html
index 9989c4c..9ce3514 100644
--- a/reference/layer_point-method.html
+++ b/reference/layer_point-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_point(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_square-method.html b/reference/layer_square-method.html
index 246c7c6..bca96f3 100644
--- a/reference/layer_square-method.html
+++ b/reference/layer_square-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_square(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_star-method.html b/reference/layer_star-method.html
index c6b7ace..08093fc 100644
--- a/reference/layer_star-method.html
+++ b/reference/layer_star-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_star(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_text-method.html b/reference/layer_text-method.html
index 7270b34..93e478b 100644
--- a/reference/layer_text-method.html
+++ b/reference/layer_text-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of texts above the heatmap tiles to a `InputHeatmap`, that on
layer_text(.data, ..., .value, .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -96,6 +100,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/parse_formula.html b/reference/parse_formula.html
index 5ae7f62..62286c5 100644
--- a/reference/parse_formula.html
+++ b/reference/parse_formula.html
@@ -17,7 +17,7 @@
diff --git a/reference/pasilla.html b/reference/pasilla.html
index 1061f28..7d80340 100644
--- a/reference/pasilla.html
+++ b/reference/pasilla.html
@@ -17,7 +17,7 @@
@@ -67,6 +67,16 @@ Example data set Pasilla
Format
Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -107,6 +111,12 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/add_class.html b/reference/add_class.html index b24d545..a12ec5b 100644 --- a/reference/add_class.html +++ b/reference/add_class.html @@ -17,7 +17,7 @@Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -100,6 +104,12 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/add_point-method.html b/reference/add_point-method.html index c046259..11b5d4c 100644 --- a/reference/add_point-method.html +++ b/reference/add_point-method.html @@ -17,7 +17,7 @@DEPRECATED. Adds a point annotation layer to a `InputHeatmap`, that on evalu
add_point(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/add_tile-method.html b/reference/add_tile-method.html
index 7a3c633..3a3453b 100644
--- a/reference/add_tile-method.html
+++ b/reference/add_tile-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ DEPRECATED. Adds a tile annotation layer to a `InputHeatmap`, that on evalua
add_tile(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/annot_to_list.html b/reference/annot_to_list.html
index 5df2c5b..da9afef 100644
--- a/reference/annot_to_list.html
+++ b/reference/annot_to_list.html
@@ -17,7 +17,7 @@
diff --git a/reference/annotation_bar-method.html b/reference/annotation_bar-method.html
index c9a5f23..a5aa7e6 100644
--- a/reference/annotation_bar-method.html
+++ b/reference/annotation_bar-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a bar annotation layer to a `InputHeatmap`, that on evaluation creates
annotation_bar(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/annotation_line-method.html b/reference/annotation_line-method.html
index 4d6db8c..cc6ab1d 100644
--- a/reference/annotation_line-method.html
+++ b/reference/annotation_line-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a line annotation layer to a `InputHeatmap`, that on evaluation creates
annotation_line(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/annotation_point-method.html b/reference/annotation_point-method.html
index 39a3631..64c06ef 100644
--- a/reference/annotation_point-method.html
+++ b/reference/annotation_point-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a point annotation layer to a `InputHeatmap`, that on evaluation create
annotation_point(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/annotation_tile-method.html b/reference/annotation_tile-method.html
index a82469f..426e717 100644
--- a/reference/annotation_tile-method.html
+++ b/reference/annotation_tile-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a tile annotation layer to a `InputHeatmap`, that on evaluation creates
annotation_tile(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/as_ComplexHeatmap-method.html b/reference/as_ComplexHeatmap-method.html
index 575f030..dc31276 100644
--- a/reference/as_ComplexHeatmap-method.html
+++ b/reference/as_ComplexHeatmap-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,11 @@ Creates a `ComplexHeatmap` object for less standard plot manipulation (e.g.
as_ComplexHeatmap(tidyHeatmap)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -82,6 +87,15 @@ Value
Details
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/as_matrix.html b/reference/as_matrix.html
index f8c2c67..78251a2 100644
--- a/reference/as_matrix.html
+++ b/reference/as_matrix.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_counts_is_na.html b/reference/check_if_counts_is_na.html
index 78ffc42..0c30be2 100644
--- a/reference/check_if_counts_is_na.html
+++ b/reference/check_if_counts_is_na.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_duplicated_genes.html b/reference/check_if_duplicated_genes.html
index 866689e..3b976e8 100644
--- a/reference/check_if_duplicated_genes.html
+++ b/reference/check_if_duplicated_genes.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_wrong_input.html b/reference/check_if_wrong_input.html
index 8993332..5a2697d 100644
--- a/reference/check_if_wrong_input.html
+++ b/reference/check_if_wrong_input.html
@@ -17,7 +17,7 @@
diff --git a/reference/drop_class.html b/reference/drop_class.html
index 52cfec2..2172cfc 100644
--- a/reference/drop_class.html
+++ b/reference/drop_class.html
@@ -17,7 +17,7 @@
diff --git a/reference/error_if_log_transformed.html b/reference/error_if_log_transformed.html
index ee6fbc1..defd568 100644
--- a/reference/error_if_log_transformed.html
+++ b/reference/error_if_log_transformed.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_abundance_norm_if_exists.html b/reference/get_abundance_norm_if_exists.html
index e7a2174..edd351c 100644
--- a/reference/get_abundance_norm_if_exists.html
+++ b/reference/get_abundance_norm_if_exists.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements.html b/reference/get_elements.html
index e3b1670..60cf049 100644
--- a/reference/get_elements.html
+++ b/reference/get_elements.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements_features.html b/reference/get_elements_features.html
index 3455ee1..e9692b2 100644
--- a/reference/get_elements_features.html
+++ b/reference/get_elements_features.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements_features_abundance.html b/reference/get_elements_features_abundance.html
index 70c577e..39673e1 100644
--- a/reference/get_elements_features_abundance.html
+++ b/reference/get_elements_features_abundance.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_counts.html b/reference/get_sample_counts.html
index e84e325..4f757d9 100644
--- a/reference/get_sample_counts.html
+++ b/reference/get_sample_counts.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_transcript.html b/reference/get_sample_transcript.html
index 1fcba07..c195cd5 100644
--- a/reference/get_sample_transcript.html
+++ b/reference/get_sample_transcript.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_transcript_counts.html b/reference/get_sample_transcript_counts.html
index 47f42db..095bd16 100644
--- a/reference/get_sample_transcript_counts.html
+++ b/reference/get_sample_transcript_counts.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_x_y_annotation_columns.html b/reference/get_x_y_annotation_columns.html
index b26bbd8..746ba88 100644
--- a/reference/get_x_y_annotation_columns.html
+++ b/reference/get_x_y_annotation_columns.html
@@ -17,7 +17,7 @@
diff --git a/reference/heatmap-method.html b/reference/heatmap-method.html
index 18c355d..b5fb9a4 100644
--- a/reference/heatmap-method.html
+++ b/reference/heatmap-method.html
@@ -17,7 +17,7 @@
@@ -115,6 +115,10 @@ Creates a `InputHeatmap` object from `tbl_df` on evaluation creates a `Compl
)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -171,6 +175,12 @@ Details
This function takes a tbl as an input and creates a `ComplexHeatmap` plot. The information is stored in a `InputHeatmap` object that is updated along the pipe statement, for example adding annotation layers.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/ifelse2_pipe.html b/reference/ifelse2_pipe.html
index 14b24ad..3af0be6 100644
--- a/reference/ifelse2_pipe.html
+++ b/reference/ifelse2_pipe.html
@@ -17,7 +17,7 @@
diff --git a/reference/ifelse_pipe.html b/reference/ifelse_pipe.html
index cc63a57..f67868e 100644
--- a/reference/ifelse_pipe.html
+++ b/reference/ifelse_pipe.html
@@ -17,7 +17,7 @@
diff --git a/reference/index.html b/reference/index.html
index fe03263..82f5113 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
diff --git a/reference/input_heatmap.html b/reference/input_heatmap.html
index 9e00831..c2050e8 100644
--- a/reference/input_heatmap.html
+++ b/reference/input_heatmap.html
@@ -17,7 +17,7 @@
@@ -73,6 +73,10 @@ input_heatmap
)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -121,6 +125,12 @@ Value
Details
To be added.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_arrow_down(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_arrow_up-method.html b/reference/layer_arrow_up-method.html
index ec48ffb..a2c1c16 100644
--- a/reference/layer_arrow_up-method.html
+++ b/reference/layer_arrow_up-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_arrow_up(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_asterisk-method.html b/reference/layer_asterisk-method.html
index 4969843..77d5973 100644
--- a/reference/layer_asterisk-method.html
+++ b/reference/layer_asterisk-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_asterisk(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_diamond-method.html b/reference/layer_diamond-method.html
index 30bb1dd..fedbb88 100644
--- a/reference/layer_diamond-method.html
+++ b/reference/layer_diamond-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_diamond(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_point-method.html b/reference/layer_point-method.html
index 9989c4c..9ce3514 100644
--- a/reference/layer_point-method.html
+++ b/reference/layer_point-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_point(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_square-method.html b/reference/layer_square-method.html
index 246c7c6..bca96f3 100644
--- a/reference/layer_square-method.html
+++ b/reference/layer_square-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_square(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_star-method.html b/reference/layer_star-method.html
index c6b7ace..08093fc 100644
--- a/reference/layer_star-method.html
+++ b/reference/layer_star-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_star(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_text-method.html b/reference/layer_text-method.html
index 7270b34..93e478b 100644
--- a/reference/layer_text-method.html
+++ b/reference/layer_text-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of texts above the heatmap tiles to a `InputHeatmap`, that on
layer_text(.data, ..., .value, .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -96,6 +100,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/parse_formula.html b/reference/parse_formula.html
index 5ae7f62..62286c5 100644
--- a/reference/parse_formula.html
+++ b/reference/parse_formula.html
@@ -17,7 +17,7 @@
diff --git a/reference/pasilla.html b/reference/pasilla.html
index 1061f28..7d80340 100644
--- a/reference/pasilla.html
+++ b/reference/pasilla.html
@@ -17,7 +17,7 @@
@@ -67,6 +67,16 @@ Example data set Pasilla
Format
Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -100,6 +104,12 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/add_tile-method.html b/reference/add_tile-method.html index 7a3c633..3a3453b 100644 --- a/reference/add_tile-method.html +++ b/reference/add_tile-method.html @@ -17,7 +17,7 @@Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -100,6 +104,12 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/annot_to_list.html b/reference/annot_to_list.html index 5df2c5b..da9afef 100644 --- a/reference/annot_to_list.html +++ b/reference/annot_to_list.html @@ -17,7 +17,7 @@Adds a bar annotation layer to a `InputHeatmap`, that on evaluation creates
annotation_bar(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/annotation_line-method.html b/reference/annotation_line-method.html
index 4d6db8c..cc6ab1d 100644
--- a/reference/annotation_line-method.html
+++ b/reference/annotation_line-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a line annotation layer to a `InputHeatmap`, that on evaluation creates
annotation_line(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/annotation_point-method.html b/reference/annotation_point-method.html
index 39a3631..64c06ef 100644
--- a/reference/annotation_point-method.html
+++ b/reference/annotation_point-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a point annotation layer to a `InputHeatmap`, that on evaluation create
annotation_point(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/annotation_tile-method.html b/reference/annotation_tile-method.html
index a82469f..426e717 100644
--- a/reference/annotation_tile-method.html
+++ b/reference/annotation_tile-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a tile annotation layer to a `InputHeatmap`, that on evaluation creates
annotation_tile(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/as_ComplexHeatmap-method.html b/reference/as_ComplexHeatmap-method.html
index 575f030..dc31276 100644
--- a/reference/as_ComplexHeatmap-method.html
+++ b/reference/as_ComplexHeatmap-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,11 @@ Creates a `ComplexHeatmap` object for less standard plot manipulation (e.g.
as_ComplexHeatmap(tidyHeatmap)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -82,6 +87,15 @@ Value
Details
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/as_matrix.html b/reference/as_matrix.html
index f8c2c67..78251a2 100644
--- a/reference/as_matrix.html
+++ b/reference/as_matrix.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_counts_is_na.html b/reference/check_if_counts_is_na.html
index 78ffc42..0c30be2 100644
--- a/reference/check_if_counts_is_na.html
+++ b/reference/check_if_counts_is_na.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_duplicated_genes.html b/reference/check_if_duplicated_genes.html
index 866689e..3b976e8 100644
--- a/reference/check_if_duplicated_genes.html
+++ b/reference/check_if_duplicated_genes.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_wrong_input.html b/reference/check_if_wrong_input.html
index 8993332..5a2697d 100644
--- a/reference/check_if_wrong_input.html
+++ b/reference/check_if_wrong_input.html
@@ -17,7 +17,7 @@
diff --git a/reference/drop_class.html b/reference/drop_class.html
index 52cfec2..2172cfc 100644
--- a/reference/drop_class.html
+++ b/reference/drop_class.html
@@ -17,7 +17,7 @@
diff --git a/reference/error_if_log_transformed.html b/reference/error_if_log_transformed.html
index ee6fbc1..defd568 100644
--- a/reference/error_if_log_transformed.html
+++ b/reference/error_if_log_transformed.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_abundance_norm_if_exists.html b/reference/get_abundance_norm_if_exists.html
index e7a2174..edd351c 100644
--- a/reference/get_abundance_norm_if_exists.html
+++ b/reference/get_abundance_norm_if_exists.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements.html b/reference/get_elements.html
index e3b1670..60cf049 100644
--- a/reference/get_elements.html
+++ b/reference/get_elements.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements_features.html b/reference/get_elements_features.html
index 3455ee1..e9692b2 100644
--- a/reference/get_elements_features.html
+++ b/reference/get_elements_features.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements_features_abundance.html b/reference/get_elements_features_abundance.html
index 70c577e..39673e1 100644
--- a/reference/get_elements_features_abundance.html
+++ b/reference/get_elements_features_abundance.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_counts.html b/reference/get_sample_counts.html
index e84e325..4f757d9 100644
--- a/reference/get_sample_counts.html
+++ b/reference/get_sample_counts.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_transcript.html b/reference/get_sample_transcript.html
index 1fcba07..c195cd5 100644
--- a/reference/get_sample_transcript.html
+++ b/reference/get_sample_transcript.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_transcript_counts.html b/reference/get_sample_transcript_counts.html
index 47f42db..095bd16 100644
--- a/reference/get_sample_transcript_counts.html
+++ b/reference/get_sample_transcript_counts.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_x_y_annotation_columns.html b/reference/get_x_y_annotation_columns.html
index b26bbd8..746ba88 100644
--- a/reference/get_x_y_annotation_columns.html
+++ b/reference/get_x_y_annotation_columns.html
@@ -17,7 +17,7 @@
diff --git a/reference/heatmap-method.html b/reference/heatmap-method.html
index 18c355d..b5fb9a4 100644
--- a/reference/heatmap-method.html
+++ b/reference/heatmap-method.html
@@ -17,7 +17,7 @@
@@ -115,6 +115,10 @@ Creates a `InputHeatmap` object from `tbl_df` on evaluation creates a `Compl
)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -171,6 +175,12 @@ Details
This function takes a tbl as an input and creates a `ComplexHeatmap` plot. The information is stored in a `InputHeatmap` object that is updated along the pipe statement, for example adding annotation layers.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/ifelse2_pipe.html b/reference/ifelse2_pipe.html
index 14b24ad..3af0be6 100644
--- a/reference/ifelse2_pipe.html
+++ b/reference/ifelse2_pipe.html
@@ -17,7 +17,7 @@
diff --git a/reference/ifelse_pipe.html b/reference/ifelse_pipe.html
index cc63a57..f67868e 100644
--- a/reference/ifelse_pipe.html
+++ b/reference/ifelse_pipe.html
@@ -17,7 +17,7 @@
diff --git a/reference/index.html b/reference/index.html
index fe03263..82f5113 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
diff --git a/reference/input_heatmap.html b/reference/input_heatmap.html
index 9e00831..c2050e8 100644
--- a/reference/input_heatmap.html
+++ b/reference/input_heatmap.html
@@ -17,7 +17,7 @@
@@ -73,6 +73,10 @@ input_heatmap
)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -121,6 +125,12 @@ Value
Details
To be added.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_arrow_down(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_arrow_up-method.html b/reference/layer_arrow_up-method.html
index ec48ffb..a2c1c16 100644
--- a/reference/layer_arrow_up-method.html
+++ b/reference/layer_arrow_up-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_arrow_up(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_asterisk-method.html b/reference/layer_asterisk-method.html
index 4969843..77d5973 100644
--- a/reference/layer_asterisk-method.html
+++ b/reference/layer_asterisk-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_asterisk(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_diamond-method.html b/reference/layer_diamond-method.html
index 30bb1dd..fedbb88 100644
--- a/reference/layer_diamond-method.html
+++ b/reference/layer_diamond-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_diamond(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_point-method.html b/reference/layer_point-method.html
index 9989c4c..9ce3514 100644
--- a/reference/layer_point-method.html
+++ b/reference/layer_point-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_point(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_square-method.html b/reference/layer_square-method.html
index 246c7c6..bca96f3 100644
--- a/reference/layer_square-method.html
+++ b/reference/layer_square-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_square(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_star-method.html b/reference/layer_star-method.html
index c6b7ace..08093fc 100644
--- a/reference/layer_star-method.html
+++ b/reference/layer_star-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_star(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_text-method.html b/reference/layer_text-method.html
index 7270b34..93e478b 100644
--- a/reference/layer_text-method.html
+++ b/reference/layer_text-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of texts above the heatmap tiles to a `InputHeatmap`, that on
layer_text(.data, ..., .value, .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -96,6 +100,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/parse_formula.html b/reference/parse_formula.html
index 5ae7f62..62286c5 100644
--- a/reference/parse_formula.html
+++ b/reference/parse_formula.html
@@ -17,7 +17,7 @@
diff --git a/reference/pasilla.html b/reference/pasilla.html
index 1061f28..7d80340 100644
--- a/reference/pasilla.html
+++ b/reference/pasilla.html
@@ -17,7 +17,7 @@
@@ -67,6 +67,16 @@ Example data set Pasilla
Format
Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -100,6 +104,12 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/annotation_line-method.html b/reference/annotation_line-method.html index 4d6db8c..cc6ab1d 100644 --- a/reference/annotation_line-method.html +++ b/reference/annotation_line-method.html @@ -17,7 +17,7 @@Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -100,6 +104,12 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/annotation_point-method.html b/reference/annotation_point-method.html index 39a3631..64c06ef 100644 --- a/reference/annotation_point-method.html +++ b/reference/annotation_point-method.html @@ -17,7 +17,7 @@Adds a point annotation layer to a `InputHeatmap`, that on evaluation create
annotation_point(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/annotation_tile-method.html b/reference/annotation_tile-method.html
index a82469f..426e717 100644
--- a/reference/annotation_tile-method.html
+++ b/reference/annotation_tile-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a tile annotation layer to a `InputHeatmap`, that on evaluation creates
annotation_tile(.data, .column, palette = NULL, size = NULL, ...)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -100,6 +104,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/as_ComplexHeatmap-method.html b/reference/as_ComplexHeatmap-method.html
index 575f030..dc31276 100644
--- a/reference/as_ComplexHeatmap-method.html
+++ b/reference/as_ComplexHeatmap-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,11 @@ Creates a `ComplexHeatmap` object for less standard plot manipulation (e.g.
as_ComplexHeatmap(tidyHeatmap)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -82,6 +87,15 @@ Value
Details
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/as_matrix.html b/reference/as_matrix.html
index f8c2c67..78251a2 100644
--- a/reference/as_matrix.html
+++ b/reference/as_matrix.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_counts_is_na.html b/reference/check_if_counts_is_na.html
index 78ffc42..0c30be2 100644
--- a/reference/check_if_counts_is_na.html
+++ b/reference/check_if_counts_is_na.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_duplicated_genes.html b/reference/check_if_duplicated_genes.html
index 866689e..3b976e8 100644
--- a/reference/check_if_duplicated_genes.html
+++ b/reference/check_if_duplicated_genes.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_wrong_input.html b/reference/check_if_wrong_input.html
index 8993332..5a2697d 100644
--- a/reference/check_if_wrong_input.html
+++ b/reference/check_if_wrong_input.html
@@ -17,7 +17,7 @@
diff --git a/reference/drop_class.html b/reference/drop_class.html
index 52cfec2..2172cfc 100644
--- a/reference/drop_class.html
+++ b/reference/drop_class.html
@@ -17,7 +17,7 @@
diff --git a/reference/error_if_log_transformed.html b/reference/error_if_log_transformed.html
index ee6fbc1..defd568 100644
--- a/reference/error_if_log_transformed.html
+++ b/reference/error_if_log_transformed.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_abundance_norm_if_exists.html b/reference/get_abundance_norm_if_exists.html
index e7a2174..edd351c 100644
--- a/reference/get_abundance_norm_if_exists.html
+++ b/reference/get_abundance_norm_if_exists.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements.html b/reference/get_elements.html
index e3b1670..60cf049 100644
--- a/reference/get_elements.html
+++ b/reference/get_elements.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements_features.html b/reference/get_elements_features.html
index 3455ee1..e9692b2 100644
--- a/reference/get_elements_features.html
+++ b/reference/get_elements_features.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements_features_abundance.html b/reference/get_elements_features_abundance.html
index 70c577e..39673e1 100644
--- a/reference/get_elements_features_abundance.html
+++ b/reference/get_elements_features_abundance.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_counts.html b/reference/get_sample_counts.html
index e84e325..4f757d9 100644
--- a/reference/get_sample_counts.html
+++ b/reference/get_sample_counts.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_transcript.html b/reference/get_sample_transcript.html
index 1fcba07..c195cd5 100644
--- a/reference/get_sample_transcript.html
+++ b/reference/get_sample_transcript.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_transcript_counts.html b/reference/get_sample_transcript_counts.html
index 47f42db..095bd16 100644
--- a/reference/get_sample_transcript_counts.html
+++ b/reference/get_sample_transcript_counts.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_x_y_annotation_columns.html b/reference/get_x_y_annotation_columns.html
index b26bbd8..746ba88 100644
--- a/reference/get_x_y_annotation_columns.html
+++ b/reference/get_x_y_annotation_columns.html
@@ -17,7 +17,7 @@
diff --git a/reference/heatmap-method.html b/reference/heatmap-method.html
index 18c355d..b5fb9a4 100644
--- a/reference/heatmap-method.html
+++ b/reference/heatmap-method.html
@@ -17,7 +17,7 @@
@@ -115,6 +115,10 @@ Creates a `InputHeatmap` object from `tbl_df` on evaluation creates a `Compl
)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -171,6 +175,12 @@ Details
This function takes a tbl as an input and creates a `ComplexHeatmap` plot. The information is stored in a `InputHeatmap` object that is updated along the pipe statement, for example adding annotation layers.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/ifelse2_pipe.html b/reference/ifelse2_pipe.html
index 14b24ad..3af0be6 100644
--- a/reference/ifelse2_pipe.html
+++ b/reference/ifelse2_pipe.html
@@ -17,7 +17,7 @@
diff --git a/reference/ifelse_pipe.html b/reference/ifelse_pipe.html
index cc63a57..f67868e 100644
--- a/reference/ifelse_pipe.html
+++ b/reference/ifelse_pipe.html
@@ -17,7 +17,7 @@
diff --git a/reference/index.html b/reference/index.html
index fe03263..82f5113 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
diff --git a/reference/input_heatmap.html b/reference/input_heatmap.html
index 9e00831..c2050e8 100644
--- a/reference/input_heatmap.html
+++ b/reference/input_heatmap.html
@@ -17,7 +17,7 @@
@@ -73,6 +73,10 @@ input_heatmap
)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -121,6 +125,12 @@ Value
Details
To be added.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_arrow_down(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_arrow_up-method.html b/reference/layer_arrow_up-method.html
index ec48ffb..a2c1c16 100644
--- a/reference/layer_arrow_up-method.html
+++ b/reference/layer_arrow_up-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_arrow_up(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_asterisk-method.html b/reference/layer_asterisk-method.html
index 4969843..77d5973 100644
--- a/reference/layer_asterisk-method.html
+++ b/reference/layer_asterisk-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_asterisk(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_diamond-method.html b/reference/layer_diamond-method.html
index 30bb1dd..fedbb88 100644
--- a/reference/layer_diamond-method.html
+++ b/reference/layer_diamond-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_diamond(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_point-method.html b/reference/layer_point-method.html
index 9989c4c..9ce3514 100644
--- a/reference/layer_point-method.html
+++ b/reference/layer_point-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_point(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_square-method.html b/reference/layer_square-method.html
index 246c7c6..bca96f3 100644
--- a/reference/layer_square-method.html
+++ b/reference/layer_square-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_square(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_star-method.html b/reference/layer_star-method.html
index c6b7ace..08093fc 100644
--- a/reference/layer_star-method.html
+++ b/reference/layer_star-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_star(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_text-method.html b/reference/layer_text-method.html
index 7270b34..93e478b 100644
--- a/reference/layer_text-method.html
+++ b/reference/layer_text-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of texts above the heatmap tiles to a `InputHeatmap`, that on
layer_text(.data, ..., .value, .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -96,6 +100,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/parse_formula.html b/reference/parse_formula.html
index 5ae7f62..62286c5 100644
--- a/reference/parse_formula.html
+++ b/reference/parse_formula.html
@@ -17,7 +17,7 @@
diff --git a/reference/pasilla.html b/reference/pasilla.html
index 1061f28..7d80340 100644
--- a/reference/pasilla.html
+++ b/reference/pasilla.html
@@ -17,7 +17,7 @@
@@ -67,6 +67,16 @@ Example data set Pasilla
Format
Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -100,6 +104,12 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/annotation_tile-method.html b/reference/annotation_tile-method.html index a82469f..426e717 100644 --- a/reference/annotation_tile-method.html +++ b/reference/annotation_tile-method.html @@ -17,7 +17,7 @@Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -100,6 +104,12 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/as_ComplexHeatmap-method.html b/reference/as_ComplexHeatmap-method.html index 575f030..dc31276 100644 --- a/reference/as_ComplexHeatmap-method.html +++ b/reference/as_ComplexHeatmap-method.html @@ -17,7 +17,7 @@Creates a `ComplexHeatmap` object for less standard plot manipulation (e.g.
as_ComplexHeatmap(tidyHeatmap)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -82,6 +87,15 @@ Value
Details
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/as_matrix.html b/reference/as_matrix.html
index f8c2c67..78251a2 100644
--- a/reference/as_matrix.html
+++ b/reference/as_matrix.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_counts_is_na.html b/reference/check_if_counts_is_na.html
index 78ffc42..0c30be2 100644
--- a/reference/check_if_counts_is_na.html
+++ b/reference/check_if_counts_is_na.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_duplicated_genes.html b/reference/check_if_duplicated_genes.html
index 866689e..3b976e8 100644
--- a/reference/check_if_duplicated_genes.html
+++ b/reference/check_if_duplicated_genes.html
@@ -17,7 +17,7 @@
diff --git a/reference/check_if_wrong_input.html b/reference/check_if_wrong_input.html
index 8993332..5a2697d 100644
--- a/reference/check_if_wrong_input.html
+++ b/reference/check_if_wrong_input.html
@@ -17,7 +17,7 @@
diff --git a/reference/drop_class.html b/reference/drop_class.html
index 52cfec2..2172cfc 100644
--- a/reference/drop_class.html
+++ b/reference/drop_class.html
@@ -17,7 +17,7 @@
diff --git a/reference/error_if_log_transformed.html b/reference/error_if_log_transformed.html
index ee6fbc1..defd568 100644
--- a/reference/error_if_log_transformed.html
+++ b/reference/error_if_log_transformed.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_abundance_norm_if_exists.html b/reference/get_abundance_norm_if_exists.html
index e7a2174..edd351c 100644
--- a/reference/get_abundance_norm_if_exists.html
+++ b/reference/get_abundance_norm_if_exists.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements.html b/reference/get_elements.html
index e3b1670..60cf049 100644
--- a/reference/get_elements.html
+++ b/reference/get_elements.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements_features.html b/reference/get_elements_features.html
index 3455ee1..e9692b2 100644
--- a/reference/get_elements_features.html
+++ b/reference/get_elements_features.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_elements_features_abundance.html b/reference/get_elements_features_abundance.html
index 70c577e..39673e1 100644
--- a/reference/get_elements_features_abundance.html
+++ b/reference/get_elements_features_abundance.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_counts.html b/reference/get_sample_counts.html
index e84e325..4f757d9 100644
--- a/reference/get_sample_counts.html
+++ b/reference/get_sample_counts.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_transcript.html b/reference/get_sample_transcript.html
index 1fcba07..c195cd5 100644
--- a/reference/get_sample_transcript.html
+++ b/reference/get_sample_transcript.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_sample_transcript_counts.html b/reference/get_sample_transcript_counts.html
index 47f42db..095bd16 100644
--- a/reference/get_sample_transcript_counts.html
+++ b/reference/get_sample_transcript_counts.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_x_y_annotation_columns.html b/reference/get_x_y_annotation_columns.html
index b26bbd8..746ba88 100644
--- a/reference/get_x_y_annotation_columns.html
+++ b/reference/get_x_y_annotation_columns.html
@@ -17,7 +17,7 @@
diff --git a/reference/heatmap-method.html b/reference/heatmap-method.html
index 18c355d..b5fb9a4 100644
--- a/reference/heatmap-method.html
+++ b/reference/heatmap-method.html
@@ -17,7 +17,7 @@
@@ -115,6 +115,10 @@ Creates a `InputHeatmap` object from `tbl_df` on evaluation creates a `Compl
)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -171,6 +175,12 @@ Details
This function takes a tbl as an input and creates a `ComplexHeatmap` plot. The information is stored in a `InputHeatmap` object that is updated along the pipe statement, for example adding annotation layers.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/ifelse2_pipe.html b/reference/ifelse2_pipe.html
index 14b24ad..3af0be6 100644
--- a/reference/ifelse2_pipe.html
+++ b/reference/ifelse2_pipe.html
@@ -17,7 +17,7 @@
diff --git a/reference/ifelse_pipe.html b/reference/ifelse_pipe.html
index cc63a57..f67868e 100644
--- a/reference/ifelse_pipe.html
+++ b/reference/ifelse_pipe.html
@@ -17,7 +17,7 @@
diff --git a/reference/index.html b/reference/index.html
index fe03263..82f5113 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
diff --git a/reference/input_heatmap.html b/reference/input_heatmap.html
index 9e00831..c2050e8 100644
--- a/reference/input_heatmap.html
+++ b/reference/input_heatmap.html
@@ -17,7 +17,7 @@
@@ -73,6 +73,10 @@ input_heatmap
)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -121,6 +125,12 @@ Value
Details
To be added.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_arrow_down(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_arrow_up-method.html b/reference/layer_arrow_up-method.html
index ec48ffb..a2c1c16 100644
--- a/reference/layer_arrow_up-method.html
+++ b/reference/layer_arrow_up-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_arrow_up(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_asterisk-method.html b/reference/layer_asterisk-method.html
index 4969843..77d5973 100644
--- a/reference/layer_asterisk-method.html
+++ b/reference/layer_asterisk-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_asterisk(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_diamond-method.html b/reference/layer_diamond-method.html
index 30bb1dd..fedbb88 100644
--- a/reference/layer_diamond-method.html
+++ b/reference/layer_diamond-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_diamond(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_point-method.html b/reference/layer_point-method.html
index 9989c4c..9ce3514 100644
--- a/reference/layer_point-method.html
+++ b/reference/layer_point-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_point(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_square-method.html b/reference/layer_square-method.html
index 246c7c6..bca96f3 100644
--- a/reference/layer_square-method.html
+++ b/reference/layer_square-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_square(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_star-method.html b/reference/layer_star-method.html
index c6b7ace..08093fc 100644
--- a/reference/layer_star-method.html
+++ b/reference/layer_star-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_star(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_text-method.html b/reference/layer_text-method.html
index 7270b34..93e478b 100644
--- a/reference/layer_text-method.html
+++ b/reference/layer_text-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of texts above the heatmap tiles to a `InputHeatmap`, that on
layer_text(.data, ..., .value, .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -96,6 +100,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/parse_formula.html b/reference/parse_formula.html
index 5ae7f62..62286c5 100644
--- a/reference/parse_formula.html
+++ b/reference/parse_formula.html
@@ -17,7 +17,7 @@
diff --git a/reference/pasilla.html b/reference/pasilla.html
index 1061f28..7d80340 100644
--- a/reference/pasilla.html
+++ b/reference/pasilla.html
@@ -17,7 +17,7 @@
@@ -67,6 +67,16 @@ Example data set Pasilla
Format
Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -82,6 +87,15 @@Value
Details
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/as_matrix.html b/reference/as_matrix.html index f8c2c67..78251a2 100644 --- a/reference/as_matrix.html +++ b/reference/as_matrix.html @@ -17,7 +17,7 @@Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -171,6 +175,12 @@Details
This function takes a tbl as an input and creates a `ComplexHeatmap` plot. The information is stored in a `InputHeatmap` object that is updated along the pipe statement, for example adding annotation layers.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/ifelse2_pipe.html b/reference/ifelse2_pipe.html index 14b24ad..3af0be6 100644 --- a/reference/ifelse2_pipe.html +++ b/reference/ifelse2_pipe.html @@ -17,7 +17,7 @@input_heatmap
) +Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -121,6 +125,12 @@Value
Details
To be added.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_arrow_down(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_arrow_up-method.html b/reference/layer_arrow_up-method.html
index ec48ffb..a2c1c16 100644
--- a/reference/layer_arrow_up-method.html
+++ b/reference/layer_arrow_up-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_arrow_up(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_asterisk-method.html b/reference/layer_asterisk-method.html
index 4969843..77d5973 100644
--- a/reference/layer_asterisk-method.html
+++ b/reference/layer_asterisk-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_asterisk(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_diamond-method.html b/reference/layer_diamond-method.html
index 30bb1dd..fedbb88 100644
--- a/reference/layer_diamond-method.html
+++ b/reference/layer_diamond-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_diamond(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_point-method.html b/reference/layer_point-method.html
index 9989c4c..9ce3514 100644
--- a/reference/layer_point-method.html
+++ b/reference/layer_point-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_point(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_square-method.html b/reference/layer_square-method.html
index 246c7c6..bca96f3 100644
--- a/reference/layer_square-method.html
+++ b/reference/layer_square-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_square(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_star-method.html b/reference/layer_star-method.html
index c6b7ace..08093fc 100644
--- a/reference/layer_star-method.html
+++ b/reference/layer_star-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_star(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_text-method.html b/reference/layer_text-method.html
index 7270b34..93e478b 100644
--- a/reference/layer_text-method.html
+++ b/reference/layer_text-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of texts above the heatmap tiles to a `InputHeatmap`, that on
layer_text(.data, ..., .value, .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -96,6 +100,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/parse_formula.html b/reference/parse_formula.html
index 5ae7f62..62286c5 100644
--- a/reference/parse_formula.html
+++ b/reference/parse_formula.html
@@ -17,7 +17,7 @@
diff --git a/reference/pasilla.html b/reference/pasilla.html
index 1061f28..7d80340 100644
--- a/reference/pasilla.html
+++ b/reference/pasilla.html
@@ -17,7 +17,7 @@
@@ -67,6 +67,16 @@ Example data set Pasilla
Format
Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -92,6 +96,12 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/layer_arrow_up-method.html b/reference/layer_arrow_up-method.html index ec48ffb..a2c1c16 100644 --- a/reference/layer_arrow_up-method.html +++ b/reference/layer_arrow_up-method.html @@ -17,7 +17,7 @@Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -92,6 +96,12 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/layer_asterisk-method.html b/reference/layer_asterisk-method.html index 4969843..77d5973 100644 --- a/reference/layer_asterisk-method.html +++ b/reference/layer_asterisk-method.html @@ -17,7 +17,7 @@Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_asterisk(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_diamond-method.html b/reference/layer_diamond-method.html
index 30bb1dd..fedbb88 100644
--- a/reference/layer_diamond-method.html
+++ b/reference/layer_diamond-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_diamond(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_point-method.html b/reference/layer_point-method.html
index 9989c4c..9ce3514 100644
--- a/reference/layer_point-method.html
+++ b/reference/layer_point-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_point(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_square-method.html b/reference/layer_square-method.html
index 246c7c6..bca96f3 100644
--- a/reference/layer_square-method.html
+++ b/reference/layer_square-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_square(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_star-method.html b/reference/layer_star-method.html
index c6b7ace..08093fc 100644
--- a/reference/layer_star-method.html
+++ b/reference/layer_star-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_star(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_text-method.html b/reference/layer_text-method.html
index 7270b34..93e478b 100644
--- a/reference/layer_text-method.html
+++ b/reference/layer_text-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of texts above the heatmap tiles to a `InputHeatmap`, that on
layer_text(.data, ..., .value, .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -96,6 +100,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/parse_formula.html b/reference/parse_formula.html
index 5ae7f62..62286c5 100644
--- a/reference/parse_formula.html
+++ b/reference/parse_formula.html
@@ -17,7 +17,7 @@
diff --git a/reference/pasilla.html b/reference/pasilla.html
index 1061f28..7d80340 100644
--- a/reference/pasilla.html
+++ b/reference/pasilla.html
@@ -17,7 +17,7 @@
@@ -67,6 +67,16 @@ Example data set Pasilla
Format
Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -92,6 +96,12 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/layer_diamond-method.html b/reference/layer_diamond-method.html index 30bb1dd..fedbb88 100644 --- a/reference/layer_diamond-method.html +++ b/reference/layer_diamond-method.html @@ -17,7 +17,7 @@Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -92,6 +96,12 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/layer_point-method.html b/reference/layer_point-method.html index 9989c4c..9ce3514 100644 --- a/reference/layer_point-method.html +++ b/reference/layer_point-method.html @@ -17,7 +17,7 @@Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_point(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_square-method.html b/reference/layer_square-method.html
index 246c7c6..bca96f3 100644
--- a/reference/layer_square-method.html
+++ b/reference/layer_square-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that o
layer_square(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_star-method.html b/reference/layer_star-method.html
index c6b7ace..08093fc 100644
--- a/reference/layer_star-method.html
+++ b/reference/layer_star-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_star(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_text-method.html b/reference/layer_text-method.html
index 7270b34..93e478b 100644
--- a/reference/layer_text-method.html
+++ b/reference/layer_text-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of texts above the heatmap tiles to a `InputHeatmap`, that on
layer_text(.data, ..., .value, .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -96,6 +100,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/parse_formula.html b/reference/parse_formula.html
index 5ae7f62..62286c5 100644
--- a/reference/parse_formula.html
+++ b/reference/parse_formula.html
@@ -17,7 +17,7 @@
diff --git a/reference/pasilla.html b/reference/pasilla.html
index 1061f28..7d80340 100644
--- a/reference/pasilla.html
+++ b/reference/pasilla.html
@@ -17,7 +17,7 @@
@@ -67,6 +67,16 @@ Example data set Pasilla
Format
Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -92,6 +96,12 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/layer_square-method.html b/reference/layer_square-method.html index 246c7c6..bca96f3 100644 --- a/reference/layer_square-method.html +++ b/reference/layer_square-method.html @@ -17,7 +17,7 @@Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -92,6 +96,12 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/layer_star-method.html b/reference/layer_star-method.html index c6b7ace..08093fc 100644 --- a/reference/layer_star-method.html +++ b/reference/layer_star-method.html @@ -17,7 +17,7 @@Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on
layer_star(.data, ..., .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -92,6 +96,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/layer_text-method.html b/reference/layer_text-method.html
index 7270b34..93e478b 100644
--- a/reference/layer_text-method.html
+++ b/reference/layer_text-method.html
@@ -17,7 +17,7 @@
@@ -66,6 +66,10 @@ Adds a layers of texts above the heatmap tiles to a `InputHeatmap`, that on
layer_text(.data, ..., .value, .size = NULL)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -96,6 +100,12 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/parse_formula.html b/reference/parse_formula.html
index 5ae7f62..62286c5 100644
--- a/reference/parse_formula.html
+++ b/reference/parse_formula.html
@@ -17,7 +17,7 @@
diff --git a/reference/pasilla.html b/reference/pasilla.html
index 1061f28..7d80340 100644
--- a/reference/pasilla.html
+++ b/reference/pasilla.html
@@ -17,7 +17,7 @@
@@ -67,6 +67,16 @@ Example data set Pasilla
Format
Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -92,6 +96,12 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/layer_text-method.html b/reference/layer_text-method.html index 7270b34..93e478b 100644 --- a/reference/layer_text-method.html +++ b/reference/layer_text-method.html @@ -17,7 +17,7 @@Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -96,6 +100,12 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/parse_formula.html b/reference/parse_formula.html index 5ae7f62..62286c5 100644 --- a/reference/parse_formula.html +++ b/reference/parse_formula.html @@ -17,7 +17,7 @@Example data set Pasilla
Format
An object of class tbl_df (inherits from tbl, data.frame) with 504 rows and 8 columns.
Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Save plot on PDF file
) +Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -102,6 +106,12 @@Details
It simply save an `Heatmap` to a PDF file use pdf() function in the back end
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/scale_design.html b/reference/scale_design.html index 38e2ec2..23bc01d 100644 --- a/reference/scale_design.html +++ b/reference/scale_design.html @@ -17,7 +17,7 @@Scale counts in a robust way against sd == 0
scale_robust(y)Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -75,6 +79,12 @@Arguments
Value
A scaled and centred numerical array
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Split the heatmap row-wise depending on the biggest branches in the cladogra
split_columns(.data, number_of_groups)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -99,6 +104,15 @@ Details
It uses `ComplexHeatmap` as visualisation tool.
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
diff --git a/reference/wrap_heatmap-method.html b/reference/wrap_heatmap-method.html
index 07b1d36..da670bd 100644
--- a/reference/wrap_heatmap-method.html
+++ b/reference/wrap_heatmap-method.html
@@ -23,7 +23,7 @@
@@ -92,6 +92,10 @@ Wrap tidyHeatmap (ComplexHeatmap) in a patchwork-compliant patch
)
+
+ Source
+ [Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+
Arguments
@@ -120,6 +124,12 @@ Value
A wrapped_patch object
A wrapped_patch object
+
+ References
+ Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
+ modular heatmap production based on tidy principles." Journal of Open Source Software.
+ doi:10.21105/joss.02472.
+
Examples
@@ -133,7 +143,6 @@ Examples
) |>
wrap_heatmap()
-
Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -99,6 +104,15 @@Details
It uses `ComplexHeatmap` as visualisation tool.
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
diff --git a/reference/wrap_heatmap-method.html b/reference/wrap_heatmap-method.html index 07b1d36..da670bd 100644 --- a/reference/wrap_heatmap-method.html +++ b/reference/wrap_heatmap-method.html @@ -23,7 +23,7 @@Source
+[Mangiola and Papenfuss., 2020](https://joss.theoj.org/papers/10.21105/joss.02472)
+Arguments
@@ -120,6 +124,12 @@Value
A wrapped_patch object
A wrapped_patch object
References
+Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for + modular heatmap production based on tidy principles." Journal of Open Source Software. + doi:10.21105/joss.02472.
+Examples
@@ -133,7 +143,6 @@Examples
) |> wrap_heatmap()
-