plot: x and y chromosomes are missing
-----Original Message----- I have a list with gene names, fold changes (=expression level) and chromosomes. Names fold change chromosome hz 1.5 2 If I plot fold change versus chromosome (or vice versa): plot (ch, fc) I see only the chromosomes with numbers but not those with letter (x and y). What can I do?
Make sure your chromosome column is a factor or character vector.
From your description so far, I deduce that it is numeric (you can check by saying class(chromosome) ). I am guessing that R has been told to convert chromosome to numeric. If so, R would convert X and Y to NA (that is, missing) in the process - with a warning that ought to have been obvious - because they are not numbers. That would explain why you aren't seeing them in the plot.
How you got that I don't know; the default would be to import as factor. Anyway, once you have chromosome properly imported as character or factor you can use barplot with chromosome used as labels, or plot(1:length(fc), axes=FALSE) and then add axes using axis(1, at=1:length(fc)), labels=chromosome) #or similar and axis(2)
How can I add a single line in that plot at a certain y-level.
see ?abline
Thanks Hermann [[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
*******************************************************************
This email and any attachments are confidential. Any use...{{dropped:8}}