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  • R - problem in heatmap reading

    Hi all, i'm using R to draw heatmaps... but I have a huge amount of data, around 600 genes... Did anyone could suggest me a better way to draw it? this image is to show you that the gene descritption can not be read at all... I've tryed to draw 3 separated heatmaps, with 200 genes each but it also dont work, i cant read the gene descritption it is all on top of other... I found this on the internet, search in google images.... it would be great for me to do a image like this: https://www.biomedcentral.com/conten...9-9-92-s12.bmp anyone knows a solution?

    sorry if my question is "too stupid" but i'm kind a basic user of R... this was the heatmap i get: http://postimage.org/image/asnzdlk9h/

  • #2
    you simply need to either:
    - increase the height of your device
    AND/OR
    - reduce the size of your characters

    if you post your R script it is probably easier to suggest sth..

    Comment


    • #3
      Personally, I would experiment with the cexRow value (start around 0.5 and go from there) and then save the heatmap as a pdf that I could modify further in illustrator or inkscape.
      Hope that helps.

      Comment


      • #4
        I will try those suggestions. and i will post my script here thanks for answers

        Comment


        • #5
          Code:
          genes <- read.csv("genes.csv", sep=",")
          row.names(genes) <- genes$Descritpion
          genes <- genes[,2:4]
          genes_matrix <- data.matrix(genes)
          genes_heatmap <- heatmap(genes_matrix, Rowv=NA, Colv=NA,col = heat.colors(256), scale="column", margins=c(5,10))
          
          ######or#########
          
          library(gplots)
          genes_heatmap2 <- heatmap.2(genes_matrix,trace="none",col=greenred(10))
          
          #######or##########
          
          genes_heatmap <- heatmap.2(genes_matrix, col=redgreen(75), scale="row", key=TRUE, symkey=FALSE, density.info="none", trace="none", cexRow=0.5)

          Comment


          • #6
            Originally posted by essvee View Post
            Personally, I would experiment with the cexRow value (start around 0.5 and go from there) and then save the heatmap as a pdf that I could modify further in illustrator or inkscape.
            Hope that helps.

            I've put 0.5... you advise me to put what?

            Comment


            • #7
              Originally posted by mudshark View Post
              you simply need to either:
              - increase the height of your device
              AND/OR
              - reduce the size of your characters

              if you post your R script it is probably easier to suggest sth..
              Already here my R codes

              Comment


              • #8
                Originally posted by essvee View Post
                Personally, I would experiment with the cexRow value (start around 0.5 and go from there) and then save the heatmap as a pdf that I could modify further in illustrator or inkscape.
                Hope that helps.
                changing the cexRow did not worked... :S cant read at all ... :S

                Comment


                • #9
                  Did not work? Can you please elaborate? Is it still too big/small? It should work with both heatmap and heatmap2. If it is too large still, decrease the number. Also, try looking at help(heatmap) and help(heatmap.2), you can learn a lot from the documentation.

                  Comment


                  • #10
                    Originally posted by essvee View Post
                    Did not work? Can you please elaborate? Is it still too big/small? It should work with both heatmap and heatmap2. If it is too large still, decrease the number. Also, try looking at help(heatmap) and help(heatmap.2), you can learn a lot from the documentation.
                    still too small, i choose 0.06 and the words are above other/on top again... and if I choose 0.03 for example, when I save to .pdf the words dont apear at all :S

                    Comment

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