Question

Automatic color assignment for annotations on ComplexHeatmap

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CodeAway ▴ 70

@codeaway-12991

Last seen 4.1 years ago

Hello All,

I love the ComplexHeatmap package, and have been using it to make some gene expression heatmaps. If I wish to add row annotations for genes, with each gene belonging to one of 10 clusters, how do I make automatic color assignments to the groups instead of giving them as a list manually?

I also had a bottom_annotation for the columns, with two classes as follows:

ha_column <- HeatmapAnnotation(df = data.frame(CellType=cellTYPE), col = list(CellType = c("WT" =  "black", "KO" = "green")))

It was easy to assign colors in this case.

But for the rows, I have 10 classes, and then for different data sets, the number of such row classes will change. So, it will be very helpful if I could get R to assign colors automatically instead of the manual assignments above (black and green).

Any help would be greatly appreciated!

Thanks.

complexheatmap • 5.0k views

ADD COMMENT • link 7.2 years ago CodeAway ▴ 70

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Further to my post above, I tried doing this:

ha_row <- HeatmapAnnotation(df = data.frame(Cluster=top20mrks$cluster), which="row",
                            col = list(Cluster = colorRampPalette(brewer.pal(12,"Paired"))(length(levels(top20mrks$cluster)))) )

But I got the following error:

Error in HeatmapAnnotation(df = data.frame(Cluster = top20mrks$cluster),  :
  elements in `col` should be named vectors.

So, how can I make this a named vector?

Thanks!

ADD REPLY • link 7.2 years ago CodeAway ▴ 70

1

Entering edit mode

I solved this myself as follows:

ttxx <- colorRampPalette(brewer.pal(12,"Paired"))(length(levels(top20mrks$cluster)))
names(ttxx) <- levels(top20mrks$cluster)
ha_row <- HeatmapAnnotation(df = data.frame(Cluster=top20mrks$cluster), which="row", col = list(Cluster = ttxx))

Now it works.

ADD REPLY • link 7.2 years ago CodeAway ▴ 70