Hello!

I went through the vignette and got all the errors sorted out, but I end up with odd-looking plots. I'm using three test samples, with a smaller BED file spanning only about seven chromosomes. I expected the colours to be similar to the plots shown in section 6.3 of the vignette, but instead the colours are scrambled all over, seemingly along the genomic position value?

par(mfrow=c(2,1),mar=c(4,3,2,1))
cnv.cols=c("red","orange","black","deepskyblue","blue")
plotCompiledCNV(CNV.segments=CNV.segments,seq.name="chr1",col=cnv.cols)
plotCompiledCNV(CNV.segments=CNV.segments,seq.name="chr2",col=cnv.cols)

Output svg file here: https://filebin.net/omi6hhb8wohmkdwc

Incidentally, how come the plot sides are cutting the sample names?

Thank you very much in advance!

sessionInfo( ):

R version 4.2.0 (2022-04-22)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Leap 15.3

Matrix products: default
BLAS:   /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8    
 [5] LC_MONETARY=en_GB.utf8    LC_MESSAGES=en_GB.utf8   
 [7] LC_PAPER=en_GB.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] exomeCopy_1.42.0     Rsamtools_2.12.0     Biostrings_2.64.0   
[4] XVector_0.36.0       GenomicRanges_1.48.0 GenomeInfoDb_1.32.2 
[7] IRanges_2.30.0       S4Vectors_0.34.0     BiocGenerics_0.42.0 

loaded via a namespace (and not attached):
 [1] crayon_1.5.1           bitops_1.0-7           zlibbioc_1.42.0       
 [4] BiocParallel_1.30.2    tools_4.2.0            RCurl_1.98-1.6        
 [7] parallel_4.2.0         compiler_4.2.0         BiocManager_1.30.18   
[10] tcltk_4.2.0            GenomeInfoDbData_1.2.8

I’m not sure why the plot looks this way. You may want to look at one sample at a time. Also note there are more developed tools, I haven’t touched this package since 2012 while I think other packages have undergone more development.