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rlbarter / superheat

An r package for generating beautiful and customizable heatmaps
https://rlbarter.github.io/superheat/
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superheat makes greys for hyperintense values #32

Closed jamesdalg closed 5 years ago

jamesdalg commented 6 years ago

superheat(X = submatrix,membership.rows = row_block_ids,membership.cols = col_block_ids,left.label = "cluster",bottom.label = "cluster",force.bottom.label = T,force.left.label = T, grid.hline.col = "white", grid.vline.col = "white", grid.hline.size = 2, grid.vline.size = 2,scale=T,heat.pal = c("green","black","red"),heat.pal.values = c(-0.5,0,0.5)) image

jamesdalg commented 6 years ago

image

rlbarter commented 6 years ago

In general, please provide a reproducible example so that I can run your code myself (e.g. I do not have access to submatrix so cannot see what the data looks like where the superheat function sets the color to grey).

The problem may also be that you are only providing colors for quantiles (-0.5, 0, 0.5) leaving the ranges outside that undefined (i.e. from -1 to -0.5 and from 0.5 to 1).

You can also try setting extreme.values.na = FALSE (this will set any values outside the given range to the max/min color rather than NA). You can also play with the heat.lim argument.

Many of these concepts are discussed in sections 4.2, and 4.3 of the vignette (https://rlbarter.github.io/superheat/heatmap-colormap.html#color-transitions)