From bc6b10095d17a1072270a2aa1f2af2718b03b4f8 Mon Sep 17 00:00:00 2001
From: William Hutchison <william.8191@fastmail.com>
Date: Fri, 12 Jul 2024 13:44:14 +1000
Subject: [PATCH 1/6] Fix factor level colour palette
---
R/utilities.R | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/R/utilities.R b/R/utilities.R
index c2e3d28..38f6703 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -723,7 +723,14 @@ get_top_left_annotation = function(.data_, .column, .row, .abundance, annotation
# If it is a list of colors
else
- colorRampPalette(palette_annotation$discrete[[.y]])(length(unique(.x))) %>% setNames(unique(.x))
+ if (class(.x) == "factor") {
+ color_vector <- palette_annotation$discrete[[.y]] %>% setNames(levels(.x))
+ color_vector[!is.na(names(color_vector))]
+
+ } else {
+ colorRampPalette(palette_annotation$discrete[[.y]])(length(unique(.x))) %>% setNames(unique(.x))
+ }
+
} else if (.x %>% class %in% c("integer", "numerical", "numeric", "double")){
# If is colorRamp
From 9541b344d77c096ef4f6d681bbab04ca6119fb29 Mon Sep 17 00:00:00 2001
From: William Hutchison <william.8191@fastmail.com>
Date: Fri, 12 Jul 2024 13:47:52 +1000
Subject: [PATCH 2/6] Update test images
---
.../tests/grouped-annotated-heatmap-2.svg | 10 +--
.../tests/grouped-custom-color-both.svg | 28 ++++----
tests/testthat/_snaps/tests/legend.svg | 66 ++++++++---------
tests/testthat/_snaps/tests/multi-type.svg | 10 +--
.../_snaps/tests/show-heatmap-legend.svg | 28 ++++----
.../testthat/_snaps/tests/size-annotation.svg | 72 +++++++++----------
tests/testthat/_snaps/tests/wrap-heatmap.svg | 9 +++
7 files changed, 116 insertions(+), 107 deletions(-)
diff --git a/tests/testthat/_snaps/tests/grouped-annotated-heatmap-2.svg b/tests/testthat/_snaps/tests/grouped-annotated-heatmap-2.svg
index 3b94b1c..40c04e4 100644
--- a/tests/testthat/_snaps/tests/grouped-annotated-heatmap-2.svg
+++ b/tests/testthat/_snaps/tests/grouped-annotated-heatmap-2.svg
@@ -906,15 +906,15 @@
<text transform='translate(445.19,510.31) rotate(-90)' text-anchor='end' style='font-size: 12.00px; font-family: sans;' textLength='57.38px' lengthAdjust='spacingAndGlyphs'>untreated1</text>
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<text x='189.89' y='59.78' text-anchor='middle' style='font-size: 8.00px; fill: #161616; font-family: sans;' textLength='38.25px' lengthAdjust='spacingAndGlyphs'>paired-end</text>
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-<rect x='134.70' y='62.51' width='55.19' height='14.17' style='stroke-width: 0.75; stroke: none; fill: #999999;' />
+<rect x='79.52' y='62.51' width='55.19' height='14.17' style='stroke-width: 0.75; stroke: none; fill: #377EB8;' />
+<rect x='134.70' y='62.51' width='55.19' height='14.17' style='stroke-width: 0.75; stroke: none; fill: #377EB8;' />
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<text x='385.87' y='59.78' text-anchor='middle' style='font-size: 8.00px; fill: #161616; font-family: sans;' textLength='39.58px' lengthAdjust='spacingAndGlyphs'>single-read</text>
<rect x='303.09' y='62.51' width='55.19' height='14.17' style='stroke-width: 0.75; stroke: none; fill: #E41A1C;' />
-<rect x='358.28' y='62.51' width='55.19' height='14.17' style='stroke-width: 0.75; stroke: none; fill: #999999;' />
-<rect x='413.46' y='62.51' width='55.19' height='14.17' style='stroke-width: 0.75; stroke: none; fill: #999999;' />
+<rect x='358.28' y='62.51' width='55.19' height='14.17' style='stroke-width: 0.75; stroke: none; fill: #377EB8;' />
+<rect x='413.46' y='62.51' width='55.19' height='14.17' style='stroke-width: 0.75; stroke: none; fill: #377EB8;' />
<text x='471.48' y='73.73' style='font-size: 12.00px; font-family: sans;' textLength='48.04px' lengthAdjust='spacingAndGlyphs'>condition</text>
<rect x='52.55' y='79.52' width='8.97' height='194.85' style='stroke-width: 0.75; fill: #FFFFFF;' />
<text transform='translate(59.78,176.94) rotate(-90)' text-anchor='middle' style='font-size: 8.00px; fill: #161616; font-family: sans;' textLength='41.35px' lengthAdjust='spacingAndGlyphs'>Intracellular</text>
@@ -1227,6 +1227,6 @@
<text x='672.27' y='237.13' style='font-size: 10.00px; font-family: sans;' textLength='31.13px' lengthAdjust='spacingAndGlyphs'>treated</text>
<text x='672.27' y='248.47' style='font-size: 10.00px; font-family: sans;' textLength='42.26px' lengthAdjust='spacingAndGlyphs'>untreated</text>
<rect x='658.10' y='228.02' width='11.34' height='11.34' style='stroke-width: 0.75; stroke: #FFFFFF; fill: #E41A1C;' />
-<rect x='658.10' y='239.36' width='11.34' height='11.34' style='stroke-width: 0.75; stroke: #FFFFFF; fill: #999999;' />
+<rect x='658.10' y='239.36' width='11.34' height='11.34' style='stroke-width: 0.75; stroke: #FFFFFF; fill: #377EB8;' />
</g>
</svg>
diff --git a/tests/testthat/_snaps/tests/grouped-custom-color-both.svg b/tests/testthat/_snaps/tests/grouped-custom-color-both.svg
index a081570..c9a681b 100644
--- a/tests/testthat/_snaps/tests/grouped-custom-color-both.svg
+++ b/tests/testthat/_snaps/tests/grouped-custom-color-both.svg
@@ -911,18 +911,18 @@
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<text x='461.76' y='63.76' style='font-size: 12.00px; font-family: sans;' textLength='48.04px' lengthAdjust='spacingAndGlyphs'>condition</text>
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+<rect x='242.12' y='67.72' width='54.20' height='14.17' style='stroke-width: 0.75; stroke: none; fill: #66C2A5;' />
+<rect x='296.32' y='67.72' width='54.20' height='14.17' style='stroke-width: 0.75; stroke: none; fill: #66C2A5;' />
+<rect x='350.53' y='67.72' width='54.20' height='14.17' style='stroke-width: 0.75; stroke: none; fill: #FC8D62;' />
+<rect x='404.73' y='67.72' width='54.20' height='14.17' style='stroke-width: 0.75; stroke: none; fill: #FC8D62;' />
<text x='461.76' y='78.93' style='font-size: 12.00px; font-family: sans;' textLength='22.69px' lengthAdjust='spacingAndGlyphs'>type</text>
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@@ -1235,11 +1235,11 @@
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<text x='662.55' y='286.60' style='font-size: 10.00px; font-family: sans;' textLength='47.81px' lengthAdjust='spacingAndGlyphs'>paired-end</text>
<text x='662.55' y='297.94' style='font-size: 10.00px; font-family: sans;' textLength='49.48px' lengthAdjust='spacingAndGlyphs'>single-read</text>
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</g>
</svg>
diff --git a/tests/testthat/_snaps/tests/legend.svg b/tests/testthat/_snaps/tests/legend.svg
index 209c4a6..d638904 100644
--- a/tests/testthat/_snaps/tests/legend.svg
+++ b/tests/testthat/_snaps/tests/legend.svg
@@ -812,46 +812,46 @@
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<text x='660.44' y='63.76' style='font-size: 12.00px; font-family: sans;' textLength='25.34px' lengthAdjust='spacingAndGlyphs'>UBR</text>
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diff --git a/tests/testthat/_snaps/tests/multi-type.svg b/tests/testthat/_snaps/tests/multi-type.svg
index 73bf03d..acf29f5 100644
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diff --git a/tests/testthat/_snaps/tests/show-heatmap-legend.svg b/tests/testthat/_snaps/tests/show-heatmap-legend.svg
index 7085813..0eba09d 100644
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diff --git a/tests/testthat/_snaps/tests/size-annotation.svg b/tests/testthat/_snaps/tests/size-annotation.svg
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<text transform='translate(85.02,523.84) rotate(-90)' text-anchor='end' style='font-size: 12.00px; font-family: sans;' textLength='46.69px' lengthAdjust='spacingAndGlyphs'>Cell type</text>
<text x='625.20' y='287.09' style='font-size: 10.00px; font-weight: bold; font-family: sans;' textLength='38.91px' lengthAdjust='spacingAndGlyphs'>Cell type</text>
<text x='639.37' y='302.17' style='font-size: 10.00px; font-family: sans;' textLength='6.67px' lengthAdjust='spacingAndGlyphs'>E</text>
@@ -859,9 +859,9 @@
<text x='639.37' y='324.85' style='font-size: 10.00px; font-family: sans;' textLength='8.33px' lengthAdjust='spacingAndGlyphs'>M</text>
<text x='639.37' y='336.19' style='font-size: 10.00px; font-family: sans;' textLength='6.11px' lengthAdjust='spacingAndGlyphs'>T</text>
<rect x='625.20' y='293.06' width='11.34' height='11.34' style='stroke-width: 0.75; stroke: #FFFFFF; fill: #E41A1C;' />
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<text x='672.55' y='287.09' style='font-size: 10.00px; font-weight: bold; font-family: sans;' textLength='21.12px' lengthAdjust='spacingAndGlyphs'>UBR</text>
<text x='686.72' y='354.32' style='font-size: 10.00px; font-family: sans;' textLength='27.81px' lengthAdjust='spacingAndGlyphs'>11400</text>
<text x='686.72' y='340.36' style='font-size: 10.00px; font-family: sans;' textLength='27.81px' lengthAdjust='spacingAndGlyphs'>11420</text>
diff --git a/tests/testthat/_snaps/tests/wrap-heatmap.svg b/tests/testthat/_snaps/tests/wrap-heatmap.svg
index af3527c..00cfca6 100644
--- a/tests/testthat/_snaps/tests/wrap-heatmap.svg
+++ b/tests/testthat/_snaps/tests/wrap-heatmap.svg
@@ -40,6 +40,15 @@
</g>
<g clip-path='url(#cpMC4wMHw3MjAuMDB8MC4wMHw1NzYuMDA=)'>
</g>
+<defs>
+ <clipPath id='cpMTAuOTZ8NzA5LjA0fDI4LjI2fDU2NS4wNA=='>
+ <rect x='10.96' y='28.26' width='698.08' height='536.78' />
+ </clipPath>
+</defs>
+<g clip-path='url(#cpMTAuOTZ8NzA5LjA0fDI4LjI2fDU2NS4wNA==)'>
+</g>
+<g clip-path='url(#cpMC4wMHw3MjAuMDB8MC4wMHw1NzYuMDA=)'>
+</g>
<defs>
<clipPath id='cpMTAuOTZ8MzU0LjUyfDI4LjI2fDU2NS4wNA=='>
<rect x='10.96' y='28.26' width='343.56' height='536.78' />
From 3f29ef58cf2fe0a03b75bcc0f9085e6cbb8b71e3 Mon Sep 17 00:00:00 2001
From: William Hutchison <william.8191@fastmail.com>
Date: Fri, 12 Jul 2024 13:58:25 +1000
Subject: [PATCH 3/6] Fix R CMD check notes
---
R/methods.R | 3 +++
R/utilities.R | 2 +-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/R/methods.R b/R/methods.R
index e9cac27..aebd9c6 100644
--- a/R/methods.R
+++ b/R/methods.R
@@ -1,3 +1,6 @@
+# Specify undefined global variables for R CMD check
+utils::globalVariables(c("shape", "size", "text", ":="))
+
#the class definition
InputHeatmap<-setClass(
"InputHeatmap",
diff --git a/R/utilities.R b/R/utilities.R
index 38f6703..3ddf29c 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -723,7 +723,7 @@ get_top_left_annotation = function(.data_, .column, .row, .abundance, annotation
# If it is a list of colors
else
- if (class(.x) == "factor") {
+ if (is(.x, "factor")) {
color_vector <- palette_annotation$discrete[[.y]] %>% setNames(levels(.x))
color_vector[!is.na(names(color_vector))]
From e6c01b34c3a42a4c0dc139fece05a710e4ab5957 Mon Sep 17 00:00:00 2001
From: William Hutchison <william.8191@fastmail.com>
Date: Fri, 12 Jul 2024 13:58:52 +1000
Subject: [PATCH 4/6] Version up
---
DESCRIPTION | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 01dbf97..49314af 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Type: Package
Package: tidyHeatmap
Title: A Tidy Implementation of Heatmap
-Version: 1.10.1
+Version: 1.10.2
Authors@R:
c(person(given = "Stefano",
family = "Mangiola",
From dee3debd1a7090d865123cfd1a8e4fba98e12263 Mon Sep 17 00:00:00 2001
From: William Hutchison <william.8191@fastmail.com>
Date: Thu, 1 Aug 2024 15:47:17 +1000
Subject: [PATCH 5/6] Add test for annotation file factor colours
---
.../tests/tile-factor-custom-palette.svg | 1048 +++++++++++++++++
tests/testthat/tests.R | 23 +
2 files changed, 1071 insertions(+)
create mode 100644 tests/testthat/_snaps/tests/tile-factor-custom-palette.svg
diff --git a/tests/testthat/_snaps/tests/tile-factor-custom-palette.svg b/tests/testthat/_snaps/tests/tile-factor-custom-palette.svg
new file mode 100644
index 0000000..edaddf7
--- /dev/null
+++ b/tests/testthat/_snaps/tests/tile-factor-custom-palette.svg
@@ -0,0 +1,1048 @@
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+<defs>
+ <style type='text/css'><![CDATA[
+ .svglite line, .svglite polyline, .svglite polygon, .svglite path, .svglite rect, .svglite circle {
+ fill: none;
+ stroke: #000000;
+ stroke-linecap: round;
+ stroke-linejoin: round;
+ stroke-miterlimit: 10.00;
+ }
+ ]]></style>
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diff --git a/tests/testthat/tests.R b/tests/testthat/tests.R
index 699f7e0..f3a59b9 100644
--- a/tests/testthat/tests.R
+++ b/tests/testthat/tests.R
@@ -665,6 +665,29 @@ test_that("tile colorRamp2 palette",{
})
+test_that("annotation tile factor colour order",{
+
+ # If factor levels correctly interpreted, colour palette should read in order:
+ # "first_level", "second_level", "third_level", "fourth_level"
+
+ p =
+ tidyHeatmap::pasilla |>
+ distinct(sample) |>
+ mutate(group = rep(c("first_level", "third_level", "second_level", "fourth_level"), length.out = n())) |>
+ mutate(group = factor(group, levels = c("first_level", "second_level", "third_level", "fourth_level"))) |>
+ right_join(tidyHeatmap::pasilla, by = "sample") |>
+ tidyHeatmap::heatmap(
+ .column = sample,
+ .row = symbol,
+ .value = `count normalised adjusted log`,
+ scale = "row"
+ ) |>
+ annotation_tile(group, c("#FF004B", "#FF00FF", "#9700FF", "#2000FF"))
+
+ vdiffr::expect_doppelganger("tile factor custom palette", p)
+
+})
+
test_that("patchwork padding",{
From 9c227c79cb38f8ca65cf2c9732fd74425c8bc2c7 Mon Sep 17 00:00:00 2001
From: William Hutchison <william.8191@fastmail.com>
Date: Thu, 1 Aug 2024 15:47:34 +1000
Subject: [PATCH 6/6] Version up
---
DESCRIPTION | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 49314af..c865047 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Type: Package
Package: tidyHeatmap
Title: A Tidy Implementation of Heatmap
-Version: 1.10.2
+Version: 1.10.3
Authors@R:
c(person(given = "Stefano",
family = "Mangiola",