Plotting copy number varation: amplification and deletion data from GISTIC

Question

[missnc]

Hi there,

I have carried out GISTIC on some Agilent 244K tumour data. I now have the G-scores for the regions significantly amplified or deleted across tumour samples. I was hoping to be able to produce a plot like figure 1A in the link below (apologies, I cannot directly put the figure into this question for some reason) from the data - would anyone know of an R-package or anything else that would be helpful in producing something that looks like this?

Many thanks!

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3198787/figure/F1/

[Chirag Nepal]

Did you manage to plot it? Would you please share if you did it.

[Vasu]

Hi Chirag,

Did you produce the plot you want? Did you use an R package or any other tool? Could you please tell something about this. I need same kind of plot. Thank you

[Chirag Nepal]

I used GISTIC2 and used the figure from it. I added gene names using illustrator.

[Vasu]

Thanks for the reply. I generated a plot like this (Copy number variation plot (R package)) But this doesn't show the genes which copy number gain and loss.

[18227587469]

hi, i want to complete the figures just like above,but my data is not the sequence data but the microarray. what should i do ? please.

[Vasu]

Hi Missnc,

Did you produce the plot you want? Did you use an R package or any other tool? Could you please tell something about this. I need same kind of plot. Thank you

Answer 1

[sophiespo]

That's a RAE plot.

The tool is here: http://cbio.mskcc.org/downloads/rae/

The publication is here: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003179

The most similar thing I've found is: A: Cnv Visualisation Tools