Plotting CNV frequencies for large datasets

[manjusha-s-ghosh]

I was trying to plot the distribution of frequecnes of CNVs on Chromosome 20 over all the cancer samples registered on Progenetix. However, the CNV frequency plot seems to retrieve only 1000 samples. When I increase the number I get an error.

[mbaudis]

@manjusha-s-ghosh Thanks for the note - this should actually be posted at http://github.com/progenetix/progenetix-web/ 😃 But answering here:

• for overview CNV plots of any given entity just plot the pre-computed frequencies instead of searching for matching samples - the latter won't really work for much more than 1000 at a time
• plots can be configured with a number of parameters, at least some of which are documented in the Progenetix docs.

So plotting chromosome 20 for "all cancers" can be achieved by using NCIT:C3262 - here with some example modifications:

https://progenetix.org/cgi/PGX/cgi/collationPlots.cgi?datasetIds=progenetix&id=NCIT:C3262&chr2plot=20&value_plot_y_max=30&colorschema=bluered&size_plotimage_w_px=480