How to change heatmap 2 color range in R

Question

I m using gplot to produce a heatmap showing log2-fold changes of a treatment groups versus paired controls  With the 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 a heat map with real fold change values  i e   non Row-Z score  which is what I m after  in the Red-Black-Green color scheme that is every biologist s favorite     The actual range of log2-fold change is -3  7  with many values in the -2 -1 and  1  2 range  which appear as dark red green  respectively   This makes the whole heatmap quite dark and so difficult to interpret     Is there a way of skewing the color gradient to make it less linear  That is  so that the gradient from black to quite bright occurs over a smaller range   And   or change the color range to be asymmetric  i e   to run from -3  7  as the data does  rather than -7  7 as the scale currently does  with black still centered on zero

User · Answer

You could try to create your own color palette using the RColorBrewer package

my_palette <- colorRampPalette(c("green", "black", "red"))(n = 1000)

and see how this looks like. But I assume in your case only scaling would help if you really want to keep the black in "the middle". You can simply use my_palette instead of the redgreen()

I recommend that you check out the RColorBrewer package, they have pretty nice in-built palettes, and see interactive website for colorbrewer.

User · Answer

I think you need to set symbreaks   FALSE That should allow for asymmetrical color scales

User · Answer

I got the color range to be asymmetric simply by changing the symkey argument to FALSE  symm F symkey F symbreaks T  scale  none    Solved the color issue with colorRampPalette with the breaks argument to specify the 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  lt - 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

User · Answer

Here s another option for those not using heatmap 2  aheatmap is good    Make a sequential vector of 100 values from min to max of your input matrix  find value closest to 0 in that  make two vector of colours to and from desired midpoint  combine and use them   breaks  lt - seq from min range inputMatrix    to max range inputMatrix    length out 100  midpoint  lt - which min abs breaks - 0   rampCol1  lt - colorRampPalette c  forestgreen    darkgreen    black    midpoint  rampCol2  lt - colorRampPalette c  black    darkred    red    100- midpoint 1   rampCols  lt - c rampCol1 rampCol2

[r] How to change heatmap.2 color range in R?

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