R) Create double-labeled MDS plot

Question

I am totally new to R.
I have expression profile data which is preprocessed and combined. Looks like this (\"exp.txt\")

       STUDY_1_CANCER_1   STUDY_         


        

Answer 1

Actually, you can do this directly in default plot command which can take pch and col arguments as vectors. Use:

with(data, plot(mds, col = as.numeric(Study), pch = as.numeric(Disease), asp = 1)

You must use asp = 1 when you plot cmdscale results: both axes must be scaled similarly. You can also add xlab and ylab arguments for nicer axis labels. For adding legend and selecting plotting characters and colours, see other responses.