Entering edit mode
5.0 years ago
zizigolu
★
4.3k
Hi,
I have called somatic copy number variation from WGS for tumor and its matched model (of course related to matched normal) by scatngs
scatngs gave me 3 filee for each sample and its matched normal, one of them is this table
> head(copynumber[1:4,])
X Chromosome Position Log.R segmented.LogR BAF segmented.BAF Copy.number Minor.allele
1 rs62635286 1 13116 -1.2304076 0.001603515 0.0000 0.3176833 2 1
2 rs75454623 1 14930 -0.3908885 0.001603515 0.3548 0.3176833 2 1
3 rs806731 1 30923 NA 0.001603515 NA NA 2 1
4 rs200943160 1 49298 -0.6588803 0.001603515 0.0000 NA 2 1
Raw.copy.number
1 0.4136176
2 1.1914908
3 NA
4 0.8499854
>
I am seeing people plot something like this in their papers
I need an intuition please how to get such plot with my data. Thanks for any suggestion
Sounds like it could be a popular package, then. I'd use
ggplot2::geom_rect
with various aesthetics linked to various dataset attributes, but a package might make life easier for you. If you could give a few sample papers, we should be able to find the package being used.Thank you, people usually say how they called the copy number but not mentioning how they plot like this for example in this paper https://www.ncbi.nlm.nih.gov/pubmed/29853643 , figure 1D
It might help to email the authors. There is not much information about the tool used in the paper. Are there other papers that have a similar graph? If not, the authors might have just used custom ggplot.