R devel - Feb 2006 - Heatmap documentation (scale argument) (PR#8614)

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".