On Fri, 28 Sep 2012, David Winsemius wrote:
On Sep 28, 2012, at 4:52 PM, David Winsemius wrote:
On Sep 28, 2012, at 3:16 PM, Nick Fankhauser wrote:
Hello R-Users!
I'm using a heatmap to visualize a matrix of values between -1 and 3.
How can I set the colors so that white is zero, below zero is blue of
increasing intensity towards -1 and above zero is red of increasing intensity
towards red?
I tried like this (using the marray and gplots packages from bioconductor):
mcol <- maPalette(low="blue", mid="white", high="red",k=100)
heatmap.2(my_matrix, col=mcol)
But white does not correspond to zero, because the value distribution is not
symmetrical, so that zero is not in the middle.
Is it somehow possible to create a color palette with white centered at zero?
The way you stated it at the beginning, I thought you should want the palette
centered at 1 rather than 0:
Oopps ... should have the number of breaks match the number of colors:
test <- seq(-1,3, len=20)
shift.BR <- colorRamp(c("blue","white", "red"), bias=2)((1:20)/20)
tpal <- rgb(shift.BR, maxColorValue=255)
barplot(test,col = tpal)
The other option, instead of adjusting the palette, is to adjust the
breaks used by heatmap.2. Furthermore, I would recommend not to use a
palette with the fully saturated colors you get by the approach above.
RColorBrewer and colorspace provide better perceptually-based palettes.
Here, I use diverge_hcl() from colorspace that gives matching perceptual
weight to values of -1 and plus 1.
## data
set.seed(1)
my_matrix <- matrix(rbeta(400, 1, 2) * 4 - 1, ncol = 20)
## color and breaks
br <- seq(-3, 3, by = 0.25)
cl <- diverge_hcl(length(br) - 1, power = 1)
## heatmap
heatmap.2(my_matrix, col = cl, breaks = br)
--
David Winsemius, MD
Alameda, CA, USA
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