search

hammerlab / cohorts

Utilities for analyzing mutations and neoepitopes in patient cohorts
Apache License 2.0
20 stars 4 forks source link

Feature - plot survival by category #224

Closed jburos closed 7 years ago

jburos commented 7 years ago

building off earlier PRs, this PR adds support for a categorical variable in plot_survival.

Now, if two groups are provided, the result is plotted as if it were a float (cut at median or threshold) or boolean value:

screen shot 2017-07-06 at 8 10 03 pm

If the value contains data for more than 2 groups, a CoxPH model is fit & survival curves for each group are plotted: screen shot 2017-07-06 at 8 13 03 pm

jburos commented 7 years ago

Oops realize now I need to cherry pick these commits to avoid the warn-on-vcf-error hack

coveralls commented 7 years ago

Coverage Status

Coverage decreased (-3.4%) to 53.533% when pulling 991d4b77e4c9d1cfeae62b38549de4fb76589068 on feature-plot-by-category into 31545c4b03d9a1edd9cc543ac1f863a140e88cd8 on master.