[R] grayscale and color bars for plotting p-value matrix

Darren Weber darrenleeweber at gmail.com
Sat Mar 18 04:38:01 CET 2006


After several days of google searches, checking colormaps, R coding,
sleepless nights, etc., I would really appreciate some advice from the
experts :-)

I have a matrix of p-values.  It is possible to use "image" to display this
matrix, using a custom colormap.  I am very cautious about using colormaps
to display quantitative data like p values, because it is too easy to
generate images that mislead our perceptions of the values.  This web page
has some nice information and helpful links on this topic:

There are many choices for colors in R, can you recommend good color maps to
display p-values?

I would like to display categorical p-values.  Does anyone have a nice
colorbar to display categorical values for the common alpha levels:

0.000 <= p < 0.001
0.001 <= p < 0.01
0.010 <= p < 0.05
0.050 <= p < 0.1
0.100 <= p <= 1

The transform

pLogMatrix <-  -log10(pValueMatrix)

is useful for display of these values.  Any comments on visualizing this?

Thanks in advance,

Darren L. Weber, Ph.D.
UCSF Dept. of Radiology

PS, the attachment is a playground for this, where the p matrix is defined
for a categorical variable (on y axis) and a continuous variable (on x

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