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

[Sarah JugurnauthLittle]

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
plot(all.acgh)
 
#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)

locale:
[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




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