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morrislab / pairtree

Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneity. Pairtree focuses on scaling to many more cancer samples and cancer cell subpopulations than other algorithms, and on producing concise and informative interactive characterizations of posterior uncertainty.
MIT License
37 stars 11 forks source link

Cluster members #39

Closed OumaimaHamza closed 1 year ago

OumaimaHamza commented 1 year ago

Hi , In the results.html under Cluster stats we can see how many members are in each cluster, Is there a way to view or print-out this list of members for specific clusters ? Thank you !

ethanumn commented 1 year ago

Hi there --

Sorry for the delay in response. If you use the bin/plottree script you'll by default have the VAFs (corrected) table which shows the cluster members. You can also use the --plot=cluster_stats flag when running plottree to limit the html file to only have this table.

If you instead wanted to do something simple like output the data for each cluster into separate files, you could use (or modify) the script attached below.

extract_clusters.zip

Ethan