ComplexHeatmap log scale gradient
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4 months ago
Carab • 0

Hi all,

does anyone know if there is a way to have a Heatmap with ComplexHeatmap and a gradient log scale ?

I used

scale_fill_gradient(trans = "log",low="white", high="darkgreen")

in ggplot, but I can't find anything to use to Heatmap()

Many thanks!!!

log colours complexHeatmap • 367 views
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Sorry Carab if you get a lot of notifications about comments in this thread, there are still some glitches in the enw codebase which we are sorting out.

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4 months ago
ATpoint 52k

I guess you need https://jokergoo.github.io/ComplexHeatmap-reference/book/legends.html#continuous-legends

but if you want log scale you will probably need to transform the data itself. The legend "just plots" what you give the function.

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4 months ago
rin ▴ 40

According to the package's vignette, you can specify this as following:

library(circlize)
col_fun = colorRamp2(c(-2, 0, 2), c("green", "white", "red"))
col_fun(seq(-3, 3))
Heatmap(mat, name = "mat", col = col_fun)

That allows you to do the coloring even if your values are not centered evenly around zero.

As for the log, I believe there is no direct argument you can pass on the Heatmap() function, so you might have to do it directly on your matrix.

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