color question
Hi!
2019-02-27 22:51 -0500, Aimin Yan wrote:
I have a question about assigning color based on the value of a
matrix
The following is my matrix.
d
lateRT earlyRT NAD ciLAD
lateRT 1.000000000 0.0000000000 0.006224017 0.001260241
earlyRT 0.000000000 1.0000000000 0.001425649 0.007418436
NAD 0.006224017 0.0014256488 1.000000000 0.064653780
ciLAD 0.001260241 0.0074184361 0.064653780 1.000000000
LAD 0.006969928 0.0007096344 0.393556636 0.002483941
LAD
lateRT 0.0069699285
earlyRT 0.0007096344
NAD 0.3935566356
ciLAD 0.0024839407
LAD 1.0000000000
I want to use the following function to get heatmap and dendrogram
heatmap.2(d,trace="none",margin=c(8, 10))
but it is hard to use color to make 0.001260241 and 0.0074184361 to be visualized differently. Does anyone know how to adjust color based on these values in this matrix?
Have you tried to adapt the attribute "colorTable"? You have to store the heatmap in an object (say "hm") and the use "hm$colorTable". See the examples here: https://www.rdocumentation.org/packages/gplots/versions/3.0.1.1/topics/heatmap.2 Also take a look on the documentation. HTH, Kimmo