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No color key in my heatmap with heatmap2.

Dear all,

I would like to output the heat map with colorkey on top. However, colorkey will not be displayed when using the following command.

heatmap.2(as.matrix(data.z),
          col=colorRampPalette(c("blue3", "white", "red3")),
          scale="none",
          key=TRUE,
          symkey=FALSE,
          density.info="none",
          trace="none",
          cexRow=0.5,
          cexCol = 1,
          Colv = FALSE,
          lmat = rbind(c(0,4,0),c(2,1,0),c(0,3,0)),
          lwid=c(1,10,0.5),lhei=c(1,6,0)
          )

The error message shows the following.

Error in plot.new() : outer margins too large (figure region too small)
In addition: Warning message:
In heatmap.2(as.matrix(data.z), col = colorRampPalette(c("blue3",  :
  Discrepancy: Colv is FALSE, while dendrogram is `both'. Omitting column dendogram.

enter image description here

What problems does my command have?

Thank you

heatmap.2 rstudio r
• 5,877 views • link
updated by Ram Ram • written by Riku • Riku

1 answer

You have a 0 dimension for your bottom row height. Changing it to: lwid=c(1,10,0.5),lhei=c(3,6,1) gives a valid plot.

However, you're calling 9 positions in lmat, when there are only 4 things to plot, and you're turning off one of the dendrograms, so there's only three things to plot. heatmap.2 plots (1) heat map, (2) row dendrogram, (3) column dendrogram, and (4) key, and it does so like this: matrix(c(4,3,2,1),2,2, byrow=TRUE)

Your call to lmat adds an extra column and row to the layout. You can get essentially the same plot with:

heatmap.2(matrix(rnorm(100), 10, 10)
          , col=colorRampPalette(c("blue3", "white", "red3"))
          , scale="none"
          , key=TRUE
          , symkey=FALSE
          , density.info="none"
          , trace="none"
          , cexRow=0.5
          , cexCol = 1
          , Colv = FALSE
          , lmat=rbind(c(3,4),c(2,1))
)
• 0 views • link
written by seidel seidel

Thank you very much! I was able to solved this probem for your advices.

• 0 views • link
written by Riku • Riku

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