legend with gradient in ComplexHeatmap
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AR3513 • 0
@ar3513-11025
Last seen 13 months ago

Hello, 

I have noticed that the legend for the colors of the heatmaps it has a fix number of breaks (5). Even if I customize the colors myself to include more breaks using colorRamp2, or if I use a continuous scale,  it stills displays only 5 breaks in the legend. 

Is there anyway to change the number of breaks in the legend?

Thanks very much, 

Andrea

complexheatmap • 1.0k views
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Mike Smith ★ 5.2k
@mike-smith
Last seen 10 hours ago
EMBL Heidelberg / de.NBI

You can do this with the heatmap_legend_param argument.  First we'll create a heatmap with the example from the ComplexHeatmap vignette:

library(ComplexHeatmap)
library(circlize)

set.seed(123)

mat = cbind(rbind(matrix(rnorm(16, -1), 4), matrix(rnorm(32, 1), 8)),
            rbind(matrix(rnorm(24, 1), 4), matrix(rnorm(48, -1), 8)))

# permute the rows and columns
mat = mat[sample(nrow(mat), nrow(mat)), sample(ncol(mat), ncol(mat))]

rownames(mat) = paste0("R", 1:12)
colnames(mat) = paste0("C", 1:10)

If we plot this with the default settings it has 5 color levels in the legend e.g.

Heatmap(mat)

We can increase this like so:

Heatmap(mat, heatmap_legend_param = list(at = -5:5))

 

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AR3513 • 0
@ar3513-11025
Last seen 13 months ago

Awesome!! Thanks very much !

 

Andrea

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