Questions related to plot.cmap function

[Former user]

1. How can I use "identify" function in cmap plots do identify the indices? Something like this is useful in context of pc plots and would be great to have it work in cmap plots too.

identify(pc.xray$z[,1], pc.xray$z[,2], labels=pdbs$id)

2. plot.diff.cmap(cm1,cm2,sse=pdb) shows grey, blue and red colors points. What does the color imply here. Grey color seems to show invariant contacts. What about the blue and red color?

[Xinqiu Yao]

Hi,

I think you can still use identify() to label points, although it is a bit tricky here for matrix plot:

plot.cmap(cm1)
ind = which(cm1>0, arr.ind=TRUE)
identify(ind, labels=apply(ind, 1, paste, collapse="_"))

About question 2, yes you are right: Gray means common contacts (invariant contacts); blue and red are specific contact to cm1 and cm2, respectively. Note that you can adjust the colors by setting function arguments. Btw, this function is till experimental and so there is no documentation file. We will write it soon and put it to the man package directory.

[Lars Skjærven]

reopen if needed