Feature request: allow specification of row annotation colours in `plotHeatmap()`
Closed this issue · 7 comments
PeteHaitch commented
We have column_annotation_colors but no row_annotation_colors in plotHeatmap().
I've had uses for row annotation colours and had to revert to using pheatmap() directly to create the plot, so it seems like it could be useful to support it in plotHeatmap().
Rather than add another argument, I wonder if it'd be better to re-consider the implementation of #119 and simply use annotation_colors to cover both column_annotation_colors and row_annotation_colors (i.e. deprecate the former) and also match the argument name in the underlying call to pheatmap()?
I realise this might be attempting to shut the gate after the horse has well and truly bolted.
reprex
# Mock up some data
suppressPackageStartupMessages(library(scater))
example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)Can specify colours for column annotations via column_annotation_colors.
plotHeatmap(
example_sce,
features=rownames(example_sce)[1:10],
colour_columns_by = "Cell_Cycle",
column_annotation_colors = list(
Cell_Cycle = c("G0" = "red", "G1" = "blue", "G2M" = "black", "S" = "pink")))
However, there's no equivalent for row annotations i.e. row_annotation_colors is ignored because it's passed via ... to pheatmap() and it does not have a row_annotation_colors argument.
plotHeatmap(
example_sce,
features=rownames(example_sce)[1:10],
annotation_row = data.frame(
class = sample(1:2, 10, replace = TRUE),
row.names = rownames(example_sce)[1:10]),
row_annotation_colors = list(class = c("A" = "blue", "B" = "red")))
If instead we attempt to supply row annotation colours via pheatmap()'s annotation_colors but there is a clash and its errors out.
plotHeatmap(
example_sce,
features=rownames(example_sce)[1:10],
annotation_row = data.frame(
class = sample(c("A", "B"), 10, replace = TRUE),
row.names = rownames(example_sce)[1:10]),
annotation_colors = list(class = c("A" = "blue", "B" = "red")))
#> Error in pheatmap::pheatmap(heat.vals, color = color, breaks = color.breaks, : formal argument "annotation_colors" matched by multiple actual argumentsCreated on 2021-05-04 by the reprex package (v2.0.0)
Session info
sessioninfo::session_info()
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#> [4] /usr/lib/R/libraryPeteHaitch commented
Ping @wwhho and @dunstone-a
alanocallaghan commented
Sorry, somehow blanked this when I saw it. Can probably add both *_annotation_colorss and then c them
alanocallaghan commented
Not a reprex but runs on master
suppressPackageStartupMessages(library(scater))
example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)
rowData(example_sce)$class <- sample(c("A", "B"), nrow(example_sce), replace = TRUE)
plotHeatmap(
example_sce,
features=rownames(example_sce)[1:10],
color_rows_by = "class",
row_annotation_colors = list(class = c("A" = "blue", "B" = "red")))
PeteHaitch commented
Thanks for following up, @alanocallaghan.
A couple of questions/comments:
- What happens if a user supplies
row_annotation_colorsandcol_annotation_colorsfor an annotation that is common to both rows and columns? The example I have in mind is when making a heatmap of cluster marker genes where I may want to annotate rows by which cluster the gene is a marker for and annotate columns by which cluster the sample is a member of. If I 'handcraft' the corresponding heatmap usingpheatmap::pheatmap()then I just supply something likeannotation_colors = list(cluster = cluster_colours)and both row and column 'cluster' annotations will use the same colour palette. Here, I'm guessing I need to do something likecol_annotation_colors = list(cluster = cluster_colours), row_annotation_colors = list(cluster = cluster_colours), but https://github.com/Alanocallaghan/scater/blob/092703b2bd3dca6d97ca85b5dbe887a661388281/R/plotHeatmap.R#L217 will lead to 2 entries namedclusterinannotation_colors. If the two colour palettes are identical then its safe to do something likeannotation_colors <- unique(c(row_annotation_colors, column_annotation_colors))orannotation_colors <- intersect(row_annotation_colors, column_annotation_colors), but what happens if the user (mistakenly) supplies incompatible colour palettes? - Switching the spelling of 'colour' to 'color' in
colour_columns_bytocolor_columns_byto match other function arguments should be documented ininst/NEWS.Rdsince it's a (minor) breaking change.
alanocallaghan commented
- I considered this briefly, I think that having the same annotation name with a different key is a sufficiently bad idea that I don't want to support it. I might do
make.namesmake.unique though* - True
*also unique and intersect both drop names
PeteHaitch commented
- *True, I forgot these were lists and not vectors. I think same annotation name with same key would be good to support. What I meant by 'what happens if they are incompatible' is whether proposed code results in a warning or error message or just a weird looking plot or ... not that it should be supported
alanocallaghan commented
Going to add a warning that says basically "I assume these are both the same"