[BioC] aCGH package. Plots: X axis label problems

Sarah JugurnauthLittle Sarah.JugurnauthLittle at icr.ac.uk
Tue May 22 13:03:30 CEST 2012

Dear Bioconductor mailing list.

I am using the aCGH package (http://www.bioconductor.org/packages/release/bioc/vignettes/aCGH/inst/doc/aCGH.pdf, http://www.bioconductor.org/packages/release/bioc/manuals/aCGH/man/aCGH.pdf) to analyse some arrayCGH data.

I am trying to generate plots within the package, from my aCGH.obj (called all.acgh in my case) such as the following:

#summary plot
#basic log2 ration plot across the genome, one sample
plotGenome(all.acgh, samples=2, naut = 22,
           Y = TRUE, X= TRUE, data = log2.ratios(all.acgh),
           yScale = c(-2, 2), samplenames = sample.names(all.acgh),
           ylb = "Log2Ratio")

These generate plots with data points plotted correctly, but with the x-axis labels all bunched up on the left hand side of the plot and unreadable. These labels are supposed to delineate the different chromosomes across the genome (1-24) with each datapoint representing a log2 ratio. 

The example data provided with the package works perfectly. I have formatted by data in the exact same way. I also have no problem with the other functions I am running on my aCGH.obj.

There are no warning messages produced. 

Any help in fixing these labels would be much appreciated.  
Many thanks, 
Sarah Jugurnauth
Institute of Cancer Research.
sjugurnauthlittle at icr.ac.uk

My sessionInfo() is as follows
R version 2.14.2 (2012-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)

[1] C

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] aCGH_1.32.0      multtest_2.10.0  Biobase_2.14.0   survival_2.36-12 cluster_1.14.1  

loaded via a namespace (and not attached):
[1] MASS_7.3-16  tools_2.14.2

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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