cohorts
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hammerlab
Pretty field labels for functions
Taking (now closed) PR #116 & turning it into a feature request for discussion.
Goal
Rather than printing missense_snv_col in plots, print Missense SNV Count / MB or Missense SNV Count, depending on the params.
however
(here quoting from the PR)
This got a little complicated for the following reasons:
Once I rename a column, something like cohort.plot_boolean(on=[missense_snv_count, split_3_mos], plot_col="missense_snv_count", boolean_col="split_3_mos") won't work because "split_3_mos" is renamed.
It's non-trivial to figure out whether a function is normalizing per MB. I can hackishly inspect the arguments (fn_argnames = fn.code.co_varnames; if "normalized_per_mb" in fn_argnames), which works for e.g. snv_count, but that doesn't work for expressed_neoantigen_count, for which normalized_per_mb isn't actually an argument. I'll probably need to run the function and set state if we're normalizing.
Going to table this for now.
I think this resolved (or at least a slightly different discussion) with the new API. Now every plotting function should take a dictionary similar to { 'Nice Name' : compute_func }
Should we allow the "pretty name" versions of fields to be set at the cohort level?
Should we allow the "pretty name" versions of fields to be set at the cohort level?
I think for functions that we provide that could make sense, since we know all of those functions, i.e. snv_count, missense_snv_coun, but would hard in general, since there is not a complete collection of possible functions.
Yeah that makes sense. I was thinking of allowing a user to pass in a dictionary of pretty names on cohort creation which, if defined for a function, could be the default display name.
