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I'm visualizing a data set with the heatmap.2 function from the gplots package in R. Basically I'm performing a hierarchical clustering analysis on the original data, while forcing the heatmap to display a limited version of the data (between -3 and +3) to limit the effect of outliers on the appearance of the heatmap, while still retaining the original clustering. When I use the full data set (fullmousedatamat), it works just fine. However, when I use a partial data set (partialmousedatamat), and want to plot it using the same key as the full data set, a couple colors are dropped out of the key and I can't figure out why.

Here is a gist containing the relevant data sets and analyses:

https://gist.github.com/jeffbruce/7412f567ac57fe1721a3

Notice how the 4th color on either side of the centre white color are dropped out. This feels like a bug to me maybe. I get the following warning message which I'm not sure how to interpret: 

Warning message:
In image.default(z = matrix(z, ncol = 1), col = col, breaks = tmpbreaks,  :
  unsorted 'breaks' will be sorted before use

Thanks for your help!

user26665
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1 Answers1

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I came across the same issue and I had to go through the code for heatmap.2 to figure it out.

It turns out that symkey=T, which is the default, adds the extreme values of the data at both ends of breaks, rendering it un-sorted:

tmpbreaks <- breaks
  if (symkey) {
    max.raw <- max(abs(c(x, breaks)), na.rm = TRUE)
    min.raw <- -max.raw
    tmpbreaks[1] <- -max(abs(x), na.rm = TRUE)
    tmpbreaks[length(tmpbreaks)] <- max(abs(x), na.rm = TRUE)
  }

Therefore, the simple way to solve this is adding symkey=F if you are providing your own breaks.

pipefish
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