R: heatmap color palette

[akolman]

Hello,

I am using R to get the correlation matrix for some gene expression data. I have the correlation matrix, and I want to use a heatmap to visualize it.

I would like to use a different color palette than the default from the heatmap, something ranging from blue to red, what is the easiest way to do this?

Thanks in advance.

[ECO]

Maybe this will help. You can set the high:low colors at will:

http://learnr.wordpress.com/2010/01/26/ggplot2-quick-heatmap-plotting/

[mgogol]

You can use RColorBrewer... there's a number of pre-made palettes, one of which is called RdBu and goes from Red to White to Blue.

hmcol<-brewer.pal(11,"RdBu")
heatmap(data,col=hmcol)

You can also use something like
hmcols<-colorRampPalette(c("red","white","blue"))(256)

to get more creative with your colors.

[severin]

R heatmap.2

I am a big fan of heatmap.2 in R that you can download from CRAN gplots.

heatmap.2(as.matrix(your data),col =
colorRampPalette(c("white","green","green4","violet","purple"))(100))

This color code is also color blind friendly.

[Joann]

A handy guide to picking colors to work in gray scale

For many cases in facilitating the further use of published data presented in color, here is a technique for making your color choices so they live on in black and white 2nd gen copy.

See illustration:
"To pick colors easily discernible from each other, whether in color or converted to grayscale, spiral through the color wheel."

Bang Wong Nature Methods 7:573 (2010)
doi: 10.1038/nmeth0810-573

[Deli Çoban]

Maybe this will help. You can set the high:low colors at will:

http://learnr.wordpress.com/2010/01/...tmap-plotting/

Really thanks for your valuable contribution..