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« Thanks for making connections in 2013 | Main | What’s been happening on slideshare? »
Monday
Dec162013

Careful with that heatmap.2(), Eugene

I'm working with vacation student Jack Simpson and colleague Lauren Bragg on exploring data from the Human Microbiome Project. We've been using heatmap.2() from the gplots package in R to look at the data in all its glory...

...or horror. Like many ecological data sets, the arch-enemy of the logarithm (zero) is present (absent?) in abundance.

To show where the zeroes are lurking, we log-transformed the data and converted the resulting -Inf values to NA, thinking that these should appear as blanks, as indeed they do on this summary:

...but things got interesting when we looked at a much more detailed heatmap. At 100% zoom, the PDF output looks like:

Keep your eye on the blue rectangle that we've added to the plot as we go to 800% zoom on the PDF:

Just to be clear: we can see data at 800% zoom that appears to be missing (i.e., NA) at 100% zoom of the PDF.

Is this a bug? Is it a feature? Does the issue lie with heatmap.2() or the PDF conversion? I'm loathe to say.

It is certainly a surprise and, I think, something to be wary of.

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