mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-17 22:08:00 +08:00
711f3b7048
* initial cut at backed mode * make flask multithreading conditional on debug flag * update X access to support backed mode * lint * improve help message for backed mode * fix tests * add MatrixProxy to normalize supported matrix types * add FAQ entry for --backed * remove use of matrix.T * clean up * add ability to disable diffexp from CLI; add hueristic to detect likely slow diffexp calculation, and warn user * fix tests * do not print diffexp speed warning if diffexp is disabled * tweak wording of diffexp speed messages * add FAQ entry on --disable-diffexp * revise heuristic for warning about slow diffexp * use quick tooltip delay on diffexp button
102 lines
3.1 KiB
Python
102 lines
3.1 KiB
Python
from abc import ABCMeta, abstractmethod
|
|
|
|
"""
|
|
Sort order for methods
|
|
1. Initialize
|
|
2. Helper
|
|
3. Filter
|
|
4. Data & Metadata
|
|
5. Computation
|
|
"""
|
|
|
|
|
|
class CXGDriver(metaclass=ABCMeta):
|
|
def __init__(self, data=None, args={}):
|
|
self.config = self._get_default_config()
|
|
self.config.update(args)
|
|
if data:
|
|
self._load_data(data)
|
|
else:
|
|
self.data = None
|
|
|
|
def update(self, data=None, args={}):
|
|
self.config.update(args)
|
|
if data:
|
|
self._load_data(data)
|
|
|
|
@staticmethod
|
|
def _get_default_config():
|
|
return {
|
|
"layout": None,
|
|
"max_category_items": None,
|
|
"diffexp_lfc_cutoff": None,
|
|
"disable_diffexp": False,
|
|
"diffexp_may_be_slow": False
|
|
}
|
|
|
|
@property
|
|
def features(self):
|
|
features = {
|
|
"cluster": {"available": False},
|
|
"layout": {"obs": {"available": False}, "var": {"available": False}},
|
|
"diffexp": {"available": True, "interactiveLimit": 50000}
|
|
}
|
|
# TODO - Interactive limit should be generated from the actual available methods see GH issue #94
|
|
if self.config["layout"]:
|
|
# TODO handle "var" when gene layout becomes available
|
|
features["layout"]["obs"] = {"available": True, "interactiveLimit": 50000}
|
|
return features
|
|
|
|
@abstractmethod
|
|
def get_schema(self):
|
|
"""
|
|
Return current schema
|
|
"""
|
|
pass
|
|
|
|
@abstractmethod
|
|
def _load_data(self, data_locator):
|
|
pass
|
|
|
|
@abstractmethod
|
|
def annotation_to_fbs_matrix(self, axis, field=None):
|
|
"""
|
|
Gets annotation value for each observation
|
|
:param axis: string obs or var
|
|
:param fields: list of keys for annotation to return, returns all annotation values if not set.
|
|
:return: flatbuffer: in fbs/matrix.fbs encoding
|
|
"""
|
|
pass
|
|
|
|
@abstractmethod
|
|
def annotation_put_fbs(self, axis, fbs):
|
|
"""
|
|
Put/save FBS as user-defined labels
|
|
"""
|
|
pass
|
|
|
|
@abstractmethod
|
|
def data_frame_to_fbs_matrix(self, filter, axis):
|
|
pass
|
|
|
|
@abstractmethod
|
|
def diffexp_topN(self, obsFilter1, obsFilter2, top_n=None, interactive_limit=None):
|
|
"""
|
|
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 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 N genes and corresponding stats
|
|
"""
|
|
pass
|
|
|
|
@abstractmethod
|
|
def layout_to_fbs_matrix(self, filter):
|
|
""" same as layout, except returns a flatbuffer """
|
|
pass
|