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  • 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.

  • #2
    Maybe this will help. You can set the high:low colors at will:

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

    Comment


    • #3
      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.

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      • #4
        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.

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        • #5
          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

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          • #6
            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..

            Comment

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