[BioC] Mfuzz plot -pdf

[James W. MacDonald]

Hi Dorothy,

dorothyc wrote:
> Hi,
> 
> I'm trying to make pdf for mfuzzPlot (please see script below), but I 
> keep getting an error saying the file is not recognizable or corrupted 
> (please see attachment).  The mfuzzPlot can be displayed in R but not 
> written as a PDF?!

The plot can be written to a pdf, but you have to override some of the 
defaults, namely the insistence that plots appear in new windows.

The following works for me (using the examples for mfuzz.plot):

 > data(yeast)
 > yeastF <- filter.NA(yeast)
49 genes excluded.
 > yeastF <- fill.NA(yeastF)
 > yeastF <- standardise(yeastF)
 > cl <- mfuzz(yeastF,c=20,m=1.25)
 > pdf("Mfuzz.pdf")
 > mfuzz.plot(yeastF, cl, c(2,2), new.window = FALSE)
 > dev.off()
windows
       2

Try that and see if it works for you.

Best,

Jim



> 
> ----------------------
> mfuzzPlot <- mfuzz.plot(eset.s, cl = cl, mfrow = c(4,4), time.labels = 
> c(0,1,2,5,10,15,30,60) )
> pdf(file = paste("MfuzzPlot", sample_output, ct, mb, ".pdf", sep="_"))
> mfuzzPlot
> dev.off()
> --- or
> pdf(file = paste("MfuzzPlot", sample_output, ct, mb, ".pdf", sep="_"))
> mfuzzPlot <- mfuzz.plot(eset.s, cl = cl, mfrow = c(4,4), time.labels = 
> c(0,1,2,5,10,15,30,60) )
> dev.off()
> ___________
> 
> I'd very much appreciate your feedback.
> 
> Thanks,
> Dorothy
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826