Skip to content

Commit

Permalink
Updated tutorials
Browse files Browse the repository at this point in the history
  • Loading branch information
Ludvig Larsson committed May 5, 2021
1 parent 19353da commit 4af6496
Show file tree
Hide file tree
Showing 14 changed files with 351 additions and 268 deletions.
1 change: 0 additions & 1 deletion .Rprofile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,4 +6,3 @@ if (requireNamespace("workflowr", quietly = TRUE)) {
} else {
message("workflowr package not installed, please run install.packages(\"workflowr\") to use the workflowr functions")
}
options(workflowr.sysgit = "")
31 changes: 24 additions & 7 deletions docs/3D_visualization.html
View file

Large diffs are not rendered by default.

106 changes: 53 additions & 53 deletions docs/Manual_annotation.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -547,16 +547,16 @@ <h1 class="title toc-ignore">Manual Annotation</h1>
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomludviglaSTUtilitywebsitetreebc60b884b5d96ce650a0bff1c18abbc66bc64662targetblankbc60b88a"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://github.com/ludvigla/STUtility_web_site/tree/bc60b884b5d96ce650a0bff1c18abbc66bc64662" target="_blank">bc60b88</a> </a>
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomludviglaSTUtilitywebsitetree19353da46806fcfded570c5c86dbfc46f7bb469etargetblank19353daa"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://github.com/ludvigla/STUtility_web_site/tree/19353da46806fcfded570c5c86dbfc46f7bb469e" target="_blank">19353da</a> </a>
</p>
</div>
<div id="strongRepositoryversionstrongahrefhttpsgithubcomludviglaSTUtilitywebsitetreebc60b884b5d96ce650a0bff1c18abbc66bc64662targetblankbc60b88a" class="panel-collapse collapse">
<div id="strongRepositoryversionstrongahrefhttpsgithubcomludviglaSTUtilitywebsitetree19353da46806fcfded570c5c86dbfc46f7bb469etargetblank19353daa" class="panel-collapse collapse">
<div class="panel-body">
<p>
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
</p>
<p>
The results in this page were generated with repository version <a href="https://github.com/ludvigla/STUtility_web_site/tree/bc60b884b5d96ce650a0bff1c18abbc66bc64662" target="_blank">bc60b88</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
The results in this page were generated with repository version <a href="https://github.com/ludvigla/STUtility_web_site/tree/19353da46806fcfded570c5c86dbfc46f7bb469e" target="_blank">19353da</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
</p>
<p>
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Expand All @@ -569,7 +569,7 @@ <h1 class="title toc-ignore">Manual Annotation</h1>
Ignored: pre_data/

Unstaged changes:
Modified: analysis/image_processing.Rmd
Modified: .Rprofile

</code></pre>
<p>
Expand Down Expand Up @@ -661,57 +661,57 @@ <h1 class="title toc-ignore">Manual Annotation</h1>
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] STutility_0.1.0 ggplot2_3.3.3 Seurat_3.1.5
[1] STutility_0.1.0 ggplot2_3.3.3 Seurat_3.1.5 workflowr_1.6.2

loaded via a namespace (and not attached):
[1] uuid_0.1-4 backports_1.1.6 workflowr_1.6.2
[4] systemfonts_0.2.1 plyr_1.8.6 igraph_1.2.6
[7] lazyeval_0.2.2 sp_1.4-1 splines_4.0.5
[10] crosstalk_1.1.1 listenv_0.8.0 digest_0.6.27
[13] foreach_1.5.0 htmltools_0.5.1.1 viridis_0.5.1
[16] magick_2.3 tiff_0.1-5 gdata_2.18.0
[19] fansi_0.4.2 magrittr_2.0.1 cluster_2.1.1
[22] doParallel_1.0.15 ROCR_1.0-11 globals_0.14.0
[25] gmodels_2.18.1 jpeg_0.1-8.1 colorspace_2.0-0
[28] blob_1.2.1 ggrepel_0.9.1 xfun_0.13
[31] dplyr_1.0.5 crayon_1.4.1 jsonlite_1.7.2
[34] zeallot_0.1.0 survival_3.2-10 zoo_1.8-9
[37] iterators_1.0.12 ape_5.4-1 glue_1.4.2
[40] gtable_0.3.0 webshot_0.5.2 leiden_0.3.7
[43] future.apply_1.7.0 scales_1.1.1 DBI_1.1.0
[46] miniUI_0.1.1.1 Rcpp_1.0.6 viridisLite_0.3.0
[49] xtable_1.8-4 spData_0.3.5 units_0.6-6
[52] reticulate_1.18 spdep_1.1-3 rsvd_1.0.3
[55] akima_0.6-2 tsne_0.1-3 htmlwidgets_1.5.3
[58] httr_1.4.2 RColorBrewer_1.1-2 ellipsis_0.3.1
[61] ica_1.0-2 pkgconfig_2.0.3 uwot_0.1.10
[64] deldir_0.1-25 utf8_1.2.1 tidyselect_1.1.0
[67] rlang_0.4.10 manipulateWidget_0.10.1 reshape2_1.4.4
[70] later_1.1.0.1 munsell_0.5.0 tools_4.0.5
[73] dbscan_1.1-5 generics_0.1.0 ggridges_0.5.3
[76] evaluate_0.14 stringr_1.4.0 fastmap_1.0.1
[79] yaml_2.2.1 knitr_1.28 fs_1.5.0
[82] fitdistrplus_1.1-3 rgl_0.100.54 purrr_0.3.4
[85] RANN_2.6.1 readbitmap_0.1.5 pbapply_1.4-3
[88] future_1.21.0 nlme_3.1-152 mime_0.10
[91] ggiraph_0.7.7 compiler_4.0.5 plotly_4.9.3
[94] png_0.1-7 e1071_1.7-3 Morpho_2.8
[97] tibble_3.1.0 stringi_1.5.3 gdtools_0.2.2
[100] lattice_0.20-41 Matrix_1.3-2 classInt_0.4-3
[103] shinyjs_1.1 vctrs_0.3.7 pillar_1.5.1
[106] LearnBayes_2.15.1 lifecycle_1.0.0 lmtest_0.9-38
[109] RcppAnnoy_0.0.18 data.table_1.14.0 cowplot_1.1.1
[112] irlba_2.3.3 Rvcg_0.19.1 raster_3.1-5
[115] httpuv_1.5.2 patchwork_1.1.1 colorRamps_2.3
[118] R6_2.5.0 imager_0.42.1 promises_1.2.0.1
[121] KernSmooth_2.23-18 gridExtra_2.3 bmp_0.3
[124] parallelly_1.24.0 codetools_0.2-18 gtools_3.8.2
[127] boot_1.3-27 MASS_7.3-53.1 assertthat_0.2.1
[130] rprojroot_1.3-2 withr_2.4.1 sctransform_0.2.1
[133] expm_0.999-4 parallel_4.0.5 grid_4.0.5
[136] tidyr_1.1.3 coda_0.19-3 class_7.3-18
[139] rmarkdown_2.1 Rtsne_0.15 git2r_0.27.1
[142] sf_0.9-7 shiny_1.4.0.2 </code></pre>
[1] uuid_0.1-4 backports_1.1.6 systemfonts_0.2.1
[4] plyr_1.8.6 igraph_1.2.6 lazyeval_0.2.2
[7] sp_1.4-1 splines_4.0.5 crosstalk_1.1.1
[10] listenv_0.8.0 digest_0.6.27 foreach_1.5.0
[13] htmltools_0.5.1.1 viridis_0.5.1 magick_2.3
[16] tiff_0.1-5 gdata_2.18.0 fansi_0.4.2
[19] magrittr_2.0.1 cluster_2.1.1 doParallel_1.0.15
[22] ROCR_1.0-11 globals_0.14.0 gmodels_2.18.1
[25] jpeg_0.1-8.1 colorspace_2.0-0 blob_1.2.1
[28] ggrepel_0.9.1 xfun_0.13 dplyr_1.0.5
[31] crayon_1.4.1 jsonlite_1.7.2 zeallot_0.1.0
[34] survival_3.2-10 zoo_1.8-9 iterators_1.0.12
[37] ape_5.4-1 glue_1.4.2 gtable_0.3.0
[40] webshot_0.5.2 leiden_0.3.7 future.apply_1.7.0
[43] scales_1.1.1 DBI_1.1.0 miniUI_0.1.1.1
[46] Rcpp_1.0.6 viridisLite_0.3.0 xtable_1.8-4
[49] spData_0.3.5 units_0.6-6 reticulate_1.18
[52] spdep_1.1-3 rsvd_1.0.3 akima_0.6-2
[55] tsne_0.1-3 htmlwidgets_1.5.3 httr_1.4.2
[58] RColorBrewer_1.1-2 ellipsis_0.3.1 ica_1.0-2
[61] pkgconfig_2.0.3 uwot_0.1.10 deldir_0.1-25
[64] utf8_1.2.1 tidyselect_1.1.0 rlang_0.4.10
[67] manipulateWidget_0.10.1 reshape2_1.4.4 later_1.1.0.1
[70] munsell_0.5.0 tools_4.0.5 dbscan_1.1-5
[73] generics_0.1.0 ggridges_0.5.3 evaluate_0.14
[76] stringr_1.4.0 fastmap_1.0.1 yaml_2.2.1
[79] knitr_1.28 fs_1.5.0 fitdistrplus_1.1-3
[82] rgl_0.100.54 purrr_0.3.4 RANN_2.6.1
[85] readbitmap_0.1.5 pbapply_1.4-3 future_1.21.0
[88] nlme_3.1-152 mime_0.10 ggiraph_0.7.7
[91] compiler_4.0.5 plotly_4.9.3 png_0.1-7
[94] e1071_1.7-3 Morpho_2.8 tibble_3.1.0
[97] stringi_1.5.3 gdtools_0.2.2 lattice_0.20-41
[100] Matrix_1.3-2 classInt_0.4-3 shinyjs_1.1
[103] vctrs_0.3.7 pillar_1.5.1 LearnBayes_2.15.1
[106] lifecycle_1.0.0 lmtest_0.9-38 RcppAnnoy_0.0.18
[109] data.table_1.14.0 cowplot_1.1.1 irlba_2.3.3
[112] Rvcg_0.19.1 raster_3.1-5 httpuv_1.5.2
[115] patchwork_1.1.1 colorRamps_2.3 R6_2.5.0
[118] imager_0.42.1 promises_1.2.0.1 KernSmooth_2.23-18
[121] gridExtra_2.3 bmp_0.3 parallelly_1.24.0
[124] codetools_0.2-18 gtools_3.8.2 boot_1.3-27
[127] MASS_7.3-53.1 assertthat_0.2.1 rprojroot_1.3-2
[130] withr_2.4.1 sctransform_0.2.1 expm_0.999-4
[133] parallel_4.0.5 grid_4.0.5 tidyr_1.1.3
[136] coda_0.19-3 class_7.3-18 rmarkdown_2.1
[139] Rtsne_0.15 git2r_0.27.1 sf_0.9-7
[142] shiny_1.4.0.2 </code></pre>
</div>


Expand Down
25 changes: 21 additions & 4 deletions docs/Neighborhood.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -547,16 +547,16 @@ <h1 class="title toc-ignore">Neighborhood analysis</h1>
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomludviglaSTUtilitywebsitetree5674505e07b93159232aa2188ddad06b0a543a53targetblank5674505a"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://github.com/ludvigla/STUtility_web_site/tree/5674505e07b93159232aa2188ddad06b0a543a53" target="_blank">5674505</a> </a>
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomludviglaSTUtilitywebsitetree19353da46806fcfded570c5c86dbfc46f7bb469etargetblank19353daa"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://github.com/ludvigla/STUtility_web_site/tree/19353da46806fcfded570c5c86dbfc46f7bb469e" target="_blank">19353da</a> </a>
</p>
</div>
<div id="strongRepositoryversionstrongahrefhttpsgithubcomludviglaSTUtilitywebsitetree5674505e07b93159232aa2188ddad06b0a543a53targetblank5674505a" class="panel-collapse collapse">
<div id="strongRepositoryversionstrongahrefhttpsgithubcomludviglaSTUtilitywebsitetree19353da46806fcfded570c5c86dbfc46f7bb469etargetblank19353daa" class="panel-collapse collapse">
<div class="panel-body">
<p>
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
</p>
<p>
The results in this page were generated with repository version <a href="https://github.com/ludvigla/STUtility_web_site/tree/5674505e07b93159232aa2188ddad06b0a543a53" target="_blank">5674505</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
The results in this page were generated with repository version <a href="https://github.com/ludvigla/STUtility_web_site/tree/19353da46806fcfded570c5c86dbfc46f7bb469e" target="_blank">19353da</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
</p>
<p>
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Expand All @@ -569,7 +569,7 @@ <h1 class="title toc-ignore">Neighborhood analysis</h1>
Ignored: pre_data/

Unstaged changes:
Modified: analysis/_site.yml
Modified: .Rprofile

</code></pre>
<p>
Expand Down Expand Up @@ -613,6 +613,23 @@ <h1 class="title toc-ignore">Neighborhood analysis</h1>
html
</td>
<td>
<a href="https://rawcdn.githack.com/ludvigla/STUtility_web_site/b88bd19a462aef37fc73d0ba3bc2e524edc4370c/docs/Neighborhood.html" target="_blank">b88bd19</a>
</td>
<td>
Ludvig Larsson
</td>
<td>
2021-05-05
</td>
<td>
Build site.
</td>
</tr>
<tr>
<td>
html
</td>
<td>
<a href="https://rawcdn.githack.com/ludvigla/STUtility_web_site/e526be2e73045ba0c52eb80da41b0ffb961eb1b1/docs/Neighborhood.html" target="_blank">e526be2</a>
</td>
<td>
Expand Down
26 changes: 23 additions & 3 deletions docs/Quality_Control.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -548,16 +548,16 @@ <h1 class="title toc-ignore">Quality control</h1>
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomludviglaSTUtilitywebsitetreebc60b884b5d96ce650a0bff1c18abbc66bc64662targetblankbc60b88a"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://github.com/ludvigla/STUtility_web_site/tree/bc60b884b5d96ce650a0bff1c18abbc66bc64662" target="_blank">bc60b88</a> </a>
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomludviglaSTUtilitywebsitetree19353da46806fcfded570c5c86dbfc46f7bb469etargetblank19353daa"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://github.com/ludvigla/STUtility_web_site/tree/19353da46806fcfded570c5c86dbfc46f7bb469e" target="_blank">19353da</a> </a>
</p>
</div>
<div id="strongRepositoryversionstrongahrefhttpsgithubcomludviglaSTUtilitywebsitetreebc60b884b5d96ce650a0bff1c18abbc66bc64662targetblankbc60b88a" class="panel-collapse collapse">
<div id="strongRepositoryversionstrongahrefhttpsgithubcomludviglaSTUtilitywebsitetree19353da46806fcfded570c5c86dbfc46f7bb469etargetblank19353daa" class="panel-collapse collapse">
<div class="panel-body">
<p>
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
</p>
<p>
The results in this page were generated with repository version <a href="https://github.com/ludvigla/STUtility_web_site/tree/bc60b884b5d96ce650a0bff1c18abbc66bc64662" target="_blank">bc60b88</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
The results in this page were generated with repository version <a href="https://github.com/ludvigla/STUtility_web_site/tree/19353da46806fcfded570c5c86dbfc46f7bb469e" target="_blank">19353da</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
</p>
<p>
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Expand All @@ -569,6 +569,9 @@ <h1 class="title toc-ignore">Quality control</h1>
Ignored: analysis/manual_annotation.png
Ignored: pre_data/

Unstaged changes:
Modified: .Rprofile

</code></pre>
<p>
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
Expand Down Expand Up @@ -611,6 +614,23 @@ <h1 class="title toc-ignore">Quality control</h1>
html
</td>
<td>
<a href="https://rawcdn.githack.com/ludvigla/STUtility_web_site/19353da46806fcfded570c5c86dbfc46f7bb469e/docs/Quality_Control.html" target="_blank">19353da</a>
</td>
<td>
Ludvig Larsson
</td>
<td>
2021-05-05
</td>
<td>
Updated tutorials
</td>
</tr>
<tr>
<td>
html
</td>
<td>
<a href="https://rawcdn.githack.com/ludvigla/STUtility_web_site/b88bd19a462aef37fc73d0ba3bc2e524edc4370c/docs/Quality_Control.html" target="_blank">b88bd19</a>
</td>
<td>
Expand Down
Loading

0 comments on commit 4af6496

Please sign in to comment.