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  • ashuchawla
    Member
    • Jan 2012
    • 38
    #1

    legend for heatmaps

    I am trying to create a heat map of genes with log2foldchange values. Following is my code,

    pdf("fold_change_heatmap_top_100.pdf" , height=20, width=15)
    x <- as.matrix(fold_change_genes[fold_change_genes$gene %in% top_100 , c(2,3,4)])
    heatmap(x, margins = c(6,6) , cexCol=2 )
    dev.off()

    But I cannot see the legend for this plot. I am not sure how draw that..Could anyone please help me? I cannot use gplots::heatmap.2 as it is not installed on the cluster I am working on yet. Please suggest something.

    Thanks,
    Ashu
    Tags: None
  • mastal
    Senior Member
    • Mar 2009
    • 666
    #2
    legend for heatmaps

    have you tried typing '?heatmap' to get the help page for
    the R function heatmap.

    That should give you a list of the parameters you can use with heatmap().

    Comment

    • ashuchawla
      Member
      • Jan 2012
      • 38
      #3
      Yes I have and it doesnt tell me anything

      Comment

      • paolo.kunder
        Member
        • Aug 2011
        • 93
        #4
        why don't you try

        heatmap.2 in library gplots
        Last edited by paolo.kunder; 07-31-2013, 07:59 AM.

        Comment

        • jp.
          Senior Member
          • Jul 2013
          • 142
          #5
          can somebody answer this trouble, please?
          map colour to values in heatmap - SEQanswers
          http://seqanswers.com/forums/showthread.php?t=33023&highlight=heatmap.2
          Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

          Comment

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