mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-16 21:37:59 +08:00
57c4e9ff33
* dead code and route removal * more dead code cleanup * fix scanpy_engine tests * lint * add missing catch in filter parsing * update scanpy NaN tests * more fbs tests and dead test removal * remove forced default for content type negotiation * bit of cleanup * more fbs test cleanup * lint * remove swagger * swagger cleanup * lint * correctly handle lack of templates * more dead code removal * remove unused files * fix dev build * lint
78 lines
2.7 KiB
Python
78 lines
2.7 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, args):
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self.data = self._load_data(data)
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self.layout_method = args["layout"]
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self.diffexp_method = args["diffexp"]
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self.max_category_items = args["max_category_items"]
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self.diffexp_lfc_cutoff = args["diffexp_lfc_cutoff"]
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self.cluster = None
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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": False},
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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.layout_method:
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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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if self.diffexp_method:
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features["diffexp"] = {"available": True, "interactiveLimit": 50000}
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if self.cluster:
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features["cluster"] = {"available": True, "interactiveLimit": 50000}
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return features
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@staticmethod
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@abstractmethod
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def _load_data(data):
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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 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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