mirror of
https://github.com/chanzuckerberg/cellxgene.git
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3660a6cc27
* icons, partway * redux for values * onChange * cancel * annotations lifecycle for category names * copy categorical * edit category * add Dataframe.withColsFrom * render user annotations; default add/delete annotation category * add label name to actions * category name edit * error checking improvements * change schema field isUserAnnotation to writable * always have an unassigned label; implement delete label * implement add new label and edit label name * label current cell selection * fix select exact bug in crossfilter * clean up categorical reducer * fix tests * remove debugging printf * implement subset/reset for user annotations * undo redo support for user annotations * remove duplicate button from categories * add modal * remove obsolete duplicate annotation reducers * remove old debugging printf * connect modal to annotation create and dup * initial full-stack wiring * finish up end-to-end wiring * fix existing unit tests * fix pytests to match new schema API * remove debugging printfs * add label file rotation * remove obsolete comment * add fbs encode/decode tests * add tests for writable annotations * simplify code * fix hashing bug with FBS encoding * lint * fix smoke tests * improve error checking in Dataframe.withColsFrom * add unit test for Dataframe.withColsFrom * add unit test for Dataframe.columns and Dataframe.renameCol * fix bug in FBS encode, add better error checks, refactor * add FBS encode/decode test * add clarifying comment * clean up action type names; fix state inconsistency in crossfilter update * change autosave timer to 2.5sec * sort categorical metadata render order so it remains consistent * add temporary autogenerated label for add-new-label operation * fix hover-over label menu interference with cell highlighting * remove debugging code * add missing reducer cases & fix typo * make dataframe memoize more general purpose * add dev mode for annos * fix error on select duplicate * handle zero occupancy categories * correctly maintain unclipped AND clipped world * correctly handle zero length FBS matrix and label files * ensure all writable categorical schema contains an unassigned category * handle case where building occupancy stack for category with no members * dialog for creating label, disable button if duplicate or empty * visually separate writeable * edit category * fix edit category name * remove debugging code * fix edit annotation label * visually define unassigned, change options * Pull in requirements.txt from `master` * label currently selected cells * duplicate label * lint * fix pytest merge issues * rename --label-file to --experimental-label-file * remove debugging console log * spelling error fix; fix bug found in PR review. * lint
100 lines
3.0 KiB
Python
100 lines
3.0 KiB
Python
from abc import ABCMeta, abstractmethod
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"""
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Sort order for methods
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1. Initialize
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2. Helper
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3. Filter
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4. Data & Metadata
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5. Computation
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"""
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class CXGDriver(metaclass=ABCMeta):
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def __init__(self, data=None, args={}):
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self.config = self._get_default_config()
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self.config.update(args)
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if data:
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self._load_data(data)
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else:
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self.data = None
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def update(self, data=None, args={}):
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self.config.update(args)
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if data:
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self._load_data(data)
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@staticmethod
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def _get_default_config():
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return {
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"layout": None,
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"max_category_items": None,
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"diffexp_lfc_cutoff": None
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}
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@property
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def features(self):
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features = {
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"cluster": {"available": False},
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"layout": {"obs": {"available": False}, "var": {"available": False}},
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"diffexp": {"available": True, "interactiveLimit": 50000}
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}
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# TODO - Interactive limit should be generated from the actual available methods see GH issue #94
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if self.config["layout"]:
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# TODO handle "var" when gene layout becomes available
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features["layout"]["obs"] = {"available": True, "interactiveLimit": 50000}
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return features
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@abstractmethod
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def get_schema(self):
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"""
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Return current schema
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"""
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pass
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@abstractmethod
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def _load_data(self, data_locator):
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pass
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@abstractmethod
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def annotation_to_fbs_matrix(self, axis, field=None):
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"""
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Gets annotation value for each observation
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:param axis: string obs or var
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:param fields: list of keys for annotation to return, returns all annotation values if not set.
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:return: flatbuffer: in fbs/matrix.fbs encoding
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"""
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pass
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@abstractmethod
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def annotation_put_fbs(self, axis, fbs):
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"""
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Put/save FBS as user-defined labels
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"""
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pass
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@abstractmethod
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def data_frame_to_fbs_matrix(self, filter, axis):
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pass
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@abstractmethod
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def diffexp_topN(self, obsFilter1, obsFilter2, top_n=None, interactive_limit=None):
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"""
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Computes the top N differentially expressed variables between two observation sets. If mode
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is "TOP_N", then stats for the top N
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dataframes
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contain a subset of variables, then statistics for all variables will be returned, otherwise
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only the top N vars will be returned.
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:param obsFilter1: filter: dictionary with filter params for first set of observations
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:param obsFilter2: filter: dictionary with filter params for second set of observations
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:param top_n: Limit results to top N (Top var mode only)
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:param interactive_limit: -- don't compute if total # genes in dataframes are larger than this
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:return: top N genes and corresponding stats
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"""
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pass
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@abstractmethod
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def layout_to_fbs_matrix(self, filter):
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""" same as layout, except returns a flatbuffer """
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pass
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