Multiple Samples Data And Chromosome Ideograms From Cnv Caller

Question

[madkitty]

I have posted a similar question here : http://www.biostars.org/post/show/46740/how-to-create-such-figure-of-chromosomes/#46762

An other similar figure representing multiple samples ideograms can be found here : http://www.biostars.org/post/show/378/drawing-chromosome-ideogams-with-data/

From mouse genome mm9 I have CNV Losses and Gain from Breakdancer and CNVnator, so our data have only :

• type of CNV
• breakpoint start and end coordinates
• chromosome number
• length of the Copy Number.

Based on those data and knowing that we have 6 samples to represent on one ideogram, which software is more appropriate to have a nice ideogram of our 6 samples ?

Thanks :)

Answer 1

[Michael]

That restricts your choice to packages that support mouse chromosomes, immediately excluding e.g. the GenomeGraphs and quantsmooth bioconductor packages because they support only human ideograms, but the Gviz Bioconductor package does support genomes in Ensembl and UCSC. From the examples, it looks like it is the most efficient way of making publication ready ideograms with your data right now. Step through the examples in the package vignettes and try them out.

Here is one example that makes such a plot, I display only two data tracks but you will manage, you need to install the Gviz package in R before:

library(IRanges)
library(Gviz)
gen <- "mm9" # mouse genome
chr <- "chr7" # chromosome 7

## make some markers
anot1 = IRanges(start=runif(100, min=1, max=152524553), width=1)
anot2 = IRanges(start=runif(100, min=1, max=152524553), width=1)
## ideogram:
itrack <- IdeogramTrack(genome = gen, chromosome = chr)
## axis:
gtrack <- GenomeAxisTrack()
## plot:
atrack1 <- AnnotationTrack(anot1, chromosome = chr,
genome = gen, name = "Sample1")
atrack2 <- AnnotationTrack(anot2, chromosome = chr,
genome = gen, name = "Sample2")
plotTracks(list(itrack, gtrack, atrack1, atrack2))

[madkitty]

Thanks a lot for your helpful answer! I'm installing Gviz right now. How should I configure data for sample 1 and 2 ? And where is my input file in the code you've mentioned ? for some reason I don't see it..

[Michael]

I simply generated random data, if you want to read a GFF file, most likely the package rtracklayer will support. If it is VCF, you can use the VariantAnnotation package.

[madkitty]

Oh Thanks! I have everything on an excel spreadsheet right now. So I would input my excel data as a VCF file I guess .. Does that go instead of atrack1 & atrack2 ?

[Michael]

Simply export into a tab or comma separated file in Ecxel and use read.delim in R. Actually you will only need columns chromosome and position information. A width or end column maybe, if you have variant larger than 1 bp. I guess you can figure that out?

[madkitty]

God knows! I'm a R newbie but I can try to learn and see .. If that doesn't work out I will post a new thread :) I will check this out right now! Thanks a lot for your help!!