mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-30 04:48:12 +08:00
core library (#711)
* move app creation to function * create engine without load * flake 8 fixes * cleanup original scanpy test * add default config * handle missing data * test data changes * unify update * load data isn't static anymore * make app a class
This commit is contained in:
Charlotte Weaver
@@ -12,7 +12,7 @@ from server.app.util.errors import (
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PrepareError,
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ScanpyFileError,
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)
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from server.app.util.utils import jsonify_scanpy
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from server.app.util.utils import jsonify_scanpy, requires_data
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from server.app.scanpy_engine.diffexp import diffexp_ttest
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from server.app.util.fbs.matrix import encode_matrix_fbs
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@@ -27,17 +27,26 @@ Sort order for methods
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class ScanpyEngine(CXGDriver):
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def __init__(self, data, args):
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def __init__(self, data=None, args={}):
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super().__init__(data, args)
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self._alias_annotation_names(Axis.OBS, args["obs_names"])
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self._alias_annotation_names(Axis.VAR, args["var_names"])
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self._validate_data_types()
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self._validate_data_calculations()
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self.cell_count = self.data.shape[0]
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self.gene_count = self.data.shape[1]
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self.layout_options = ["umap", "tsne"]
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self.diffexp_options = ["ttest"]
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self._create_schema()
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if self.data:
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self._validate_and_initialize()
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def update(self, data=None, args={}):
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super().__init__(data, args)
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if self.data:
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self._validate_and_initialize()
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@staticmethod
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def _get_default_config():
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return {
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"layout": "umap",
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"diffexp": "ttest",
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"max_category_items": 100,
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"obs_names": None,
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"var_names": None,
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"diffexp_lfc_cutoff": 0.01,
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}
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def _alias_annotation_names(self, axis, name):
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"""
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@@ -95,6 +104,7 @@ class ScanpyEngine(CXGDriver):
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return True
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return False
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@requires_data
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def _create_schema(self):
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self.schema = {
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"dataframe": {
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@@ -128,13 +138,12 @@ class ScanpyEngine(CXGDriver):
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)
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self.schema["annotations"][ax].append(ann_schema)
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@staticmethod
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def _load_data(data):
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def _load_data(self, data):
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# Based on benchmarking, cache=True has no impact on perf.
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# Note: as of current scanpy/anndata release, setting backed='r' will
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# result in an error. https://github.com/theislab/anndata/issues/79
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try:
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result = sc.read(data, cache=True)
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self.data = sc.read(data, cache=True)
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except ValueError:
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raise ScanpyFileError(
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"File must be in the .h5ad format. Please read "
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@@ -151,8 +160,18 @@ class ScanpyEngine(CXGDriver):
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f"Error while loading file: {e}, File must be in the .h5ad format, please check "
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f"that your input and try again."
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)
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return result
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@requires_data
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def _validate_and_initialize(self):
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self._alias_annotation_names(Axis.OBS, self.config["obs_names"])
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self._alias_annotation_names(Axis.VAR, self.config["var_names"])
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self._validate_data_types()
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self._validate_data_calculations()
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self.cell_count = self.data.shape[0]
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self.gene_count = self.data.shape[1]
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self._create_schema()
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@requires_data
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def _validate_data_types(self):
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if self.data.X.dtype != "float32":
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warnings.warn(
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@@ -176,7 +195,7 @@ class ScanpyEngine(CXGDriver):
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)
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if isinstance(datatype, CategoricalDtype):
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category_num = len(curr_axis[ann].dtype.categories)
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if category_num > 500 and category_num > self.max_category_items:
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if category_num > 500 and category_num > self.config['max_category_items']:
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warnings.warn(
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f"{str(ax).title()} annotation '{ann}' has {category_num} categories, this may be "
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f"cumbersome or slow to display. We recommend setting the "
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@@ -184,16 +203,17 @@ class ScanpyEngine(CXGDriver):
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f"annotations with more than 500 categories in the UI"
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)
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@requires_data
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def _validate_data_calculations(self):
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layout_key = f"X_{self.layout_method}"
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layout_key = f"X_{self.config['layout']}"
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try:
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assert layout_key in self.data.obsm_keys()
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except AssertionError:
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raise PrepareError(
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f"Cannot find a field with coordinates for the {self.layout_method} layout requested. A different"
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f"Cannot find a field with coordinates for the {self.config['layout']} layout requested. A different"
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f" layout may have been computed. The requested layout must be pre-calculated and saved "
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f"back in the h5ad file. You can run "
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f"`cellxgene prepare --layout {self.layout_method} <datafile>` "
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f"`cellxgene prepare --layout {self.config['layout']} <datafile>` "
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f"to solve this problem. "
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)
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@@ -220,7 +240,7 @@ class ScanpyEngine(CXGDriver):
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mask = np.zeros((count,), dtype=bool)
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for i in filter:
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if type(i) == list:
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mask[i[0] : i[1]] = True
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mask[i[0]: i[1]] = True
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else:
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mask[i] = True
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return mask
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@@ -241,6 +261,7 @@ class ScanpyEngine(CXGDriver):
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)
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return mask
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@requires_data
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def _filter_to_mask(self, filter, use_slices=True):
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if use_slices:
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obs_selector = slice(0, self.data.n_obs)
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@@ -260,6 +281,7 @@ class ScanpyEngine(CXGDriver):
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)
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return obs_selector, var_selector
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@requires_data
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def annotation_to_fbs_matrix(self, axis, fields=None):
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if axis == Axis.OBS:
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df = self.data.obs
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@@ -269,6 +291,7 @@ class ScanpyEngine(CXGDriver):
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df = df[fields]
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return encode_matrix_fbs(df, col_idx=df.columns)
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@requires_data
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def data_frame_to_fbs_matrix(self, filter, axis):
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"""
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Retrieves data 'X' and returns in a flatbuffer Matrix.
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@@ -295,6 +318,7 @@ class ScanpyEngine(CXGDriver):
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X = X[:, var_selector]
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return encode_matrix_fbs(X, col_idx=np.nonzero(var_selector)[0], row_idx=None)
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@requires_data
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def diffexp_topN(self, obsFilterA, obsFilterB, top_n=None, interactive_limit=None):
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if Axis.VAR in obsFilterA or Axis.VAR in obsFilterB:
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raise FilterError("Observation filters may not contain vaiable conditions")
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@@ -310,7 +334,7 @@ class ScanpyEngine(CXGDriver):
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if top_n is None:
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top_n = DEFAULT_TOP_N
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result = diffexp_ttest(
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self.data, obs_mask_A, obs_mask_B, top_n, self.diffexp_lfc_cutoff
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self.data, obs_mask_A, obs_mask_B, top_n, self.config['diffexp_lfc_cutoff']
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)
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try:
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return jsonify_scanpy(result)
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@@ -319,6 +343,7 @@ class ScanpyEngine(CXGDriver):
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"Error encoding differential expression to JSON"
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)
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@requires_data
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def layout_to_fbs_matrix(self):
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"""
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Return the default 2-D layout for cells as a FBS Matrix.
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@@ -328,14 +353,14 @@ class ScanpyEngine(CXGDriver):
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* only returns Matrix in columnar layout
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"""
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try:
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full_embedding = self.data.obsm[f"X_{self.layout_method}"]
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full_embedding = self.data.obsm[f"X_{self.config['layout']}"]
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if full_embedding.shape[1] > 2:
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warnings.warn(f"Warning: found {full_embedding.shape[1]} \
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components of embedding. Using the first two for layout display.")
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df_layout = full_embedding[:, :2]
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except ValueError as e:
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raise PrepareError(
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f"Layout has not been calculated using {self.layout_method}, "
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f"Layout has not been calculated using {self.config['layout']}, "
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f"please prepare your datafile and relaunch cellxgene") from e
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normalized_layout = (df_layout - df_layout.min()) / (df_layout.max() - df_layout.min())
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