[Rd] Heatmap documentation (scale argument) (PR#8614)

From: <kwright68_at_gmail.com>
Date: Thu 16 Feb 2006 - 23:04:49 GMT


Full_Name: Kevin Wright
Version: 2.2.1
OS: Windows 2000
Submission from: (NULL) (170.54.58.4)

The help page for heatmap says this about the scale argument:

scale character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. The default is "row" if symm false, and "none" otherwise.

This is true, but not completely accurate IMHO. In particular, 'scale' has no effect on the dendrograms, since the dendrograms are calculated before any scaling is done. The scale argument only affects the colors used in the 'image' part of the heatmap.

Consider:
  x <- as.matrix(mtcars)
  heatmap(x, scale="column")
  heatmap(scale(x), scale="none")
Those two plots give different dendrograms.

It would be nice for the documentation to make this more clear. For example:

"scaling affects only the 'image' part of the heatmap and has no effect on the dendgrograms".



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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Fri Feb 17 10:07:33 2006

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