purity/ploidy information from standalone command argument
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Thank you for the great work!
Chimera-UI asks for purity information for each sample in the table format but couldn't find an option to provide in the standalone command program. Is it okay w/o the information?
One last question is that do you have any script that I can use for postprocessing analysis (phylogeny tree visualization or distance heatmap) w/ chimaera output table?
Hi @cjhong thanks a lot for using Chimaera.
Regarding the purity, the command-line interface behaves exactly like the UI. The purity is used to estimate and guess initial frequencies and its needed for the analysis with Chimaera. In case you have no putiry estimates I recommend setting a fixed value for each sample in the purity column above .95.
Unfortunately we have no script for post-processing, but using pandas and seaborn you can easily reproduce all the plots we report in the paper. We will keep in mind this comment and in case we find time, we would be happy to add those.