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R: heatmap color palette

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  • Deli Çoban
    replied
    Originally posted by ECO View Post
    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..

    Leave a comment:


  • Joann
    replied
    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

    Leave a comment:


  • severin
    replied
    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.

    Leave a comment:


  • mgogol
    replied
    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.

    Leave a comment:


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

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

    Leave a comment:


  • akolman
    started a topic R: heatmap color palette

    R: heatmap color palette

    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.
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