How to change heatmap.2 color range in R? -
i'm using gplot produce heatmap showing log2-fold changes of treatment groups versus paired controls. following code:
heatmap.2(as.matrix(seqcounttable), col=redgreen(75), density.info="none", trace="none", dendrogram=c("row"), symm=f,symkey=t,symbreaks=t, scale="none")
i output heat map real fold change values (i.e., non row-z score) i'm after, in red-black-green color scheme every biologist's favorite!
the actual range of log2-fold change -3/+7, many values in -2/-1 , +1/+2 range, appear dark red/green (respectively). makes whole heatmap quite dark , difficult interpret.
- is there way of skewing color gradient make less linear? is, gradient black quite bright occurs on smaller range?
- and / or change color range asymmetric, i.e., run -3/+7, data does, rather -7/+7 scale does, black still centered on zero?
i got color range asymmetric changing symkey argument false
symm=f,symkey=f,symbreaks=t, scale="none"
solved color issue colorramppalette breaks argument specify range of each color, e.g.
colors = c(seq(-3,-2,length=100),seq(-2,0.5,length=100),seq(0.5,6,length=100)) my_palette <- colorramppalette(c("red", "black", "green"))(n = 299)
altogether
heatmap.2(as.matrix(seqcounttable), col=my_palette, breaks=colors, density.info="none", trace="none", dendrogram=c("row"), symm=f,symkey=f,symbreaks=t, scale="none")
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