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diffexp performance & UX improvements (#431)

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* new diffexp REST API spec

* new diffexp REST API; faster diffexp and dataframe slicing

* first draft of fast diffexp

* convert variance calculation to two-pass method

* lint

* update front-end use of API

* fix typo in spec

* disable content compression

* catch index filter format errors

* clean up of dead code

* resolve PR review comments
This commit is contained in:
Bruce Martin
2018-11-14 12:51:24 -08:00
committed by GitHub
parent bc0cecbd1c
commit 00a68276a2
11 changed files with 237 additions and 227 deletions
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server/app/driver/driver.py
+7 -5
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@@ -83,16 +83,18 @@ class CXGDriver(metaclass=ABCMeta):
pass
@abstractmethod
def diffexp(self, filter1, filter2, top_n=None, interactive_limit=None):
def diffexp_topN(self, obsFilter1, obsFilter2, top_n=None, interactive_limit=None):
"""
Computes the top differentially expressed variables between two observation sets. If dataframes
Computes the top N differentially expressed variables between two observation sets. If mode
is "TOP_N", then stats for the top N
dataframes
contain a subset of variables, then statistics for all variables will be returned, otherwise
only the top N vars will be returned.
:param filter1: filter: dictionary with filter params for first set of observations
:param filter2: filter: dictionary with filter params for second set of observations
:param obsFilter1: filter: dictionary with filter params for first set of observations
:param obsFilter2: filter: dictionary with filter params for second set of observations
:param top_n: Limit results to top N (Top var mode only)
:param interactive_limit: -- don't compute if total # genes in dataframes are larger than this
:return: top genes, stats and expression values for variables
:return: top N genes and corresponding stats
"""
pass