fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-10-07 06:58:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

gene set summary progress (#2127)

Browse Source 
* revert removal of cache control headers

* checkpoint work on revising summary route

* add summary query support to annoMatrix

* summarize route cleanup

* add mising file

* clean up summarize route

* add summary histogram

* update deps

* lint

* more lint

* lint

* manage crossfiler during gene set state changes

* remove obsolete debugging code

* correctly perform async watch in histogram

* better error handling
This commit is contained in:
Bruce Martin
2021-03-30 14:43:53 -07:00
committed by GitHub
parent bfb9e1edcc
commit ae30b66123
47 changed files with 28628 additions and 9109 deletions
Download Patch File Download Diff File Expand all files Collapse all files
backend/server/data_anndata/anndata_adaptor.py
+9 -36
View File
@@ -5,7 +5,6 @@ import anndata
import numpy as np
from packaging import version
from pandas.core.dtypes.dtypes import CategoricalDtype
import pandas as pd
from scipy import sparse
from server_timing import Timing as ServerTiming
@@ -13,7 +12,7 @@ import backend.server.compute.diffexp_generic as diffexp_generic
from backend.common.colors import convert_anndata_category_colors_to_cxg_category_colors
from backend.common.constants import Axis, MAX_LAYOUTS
from backend.server.common.corpora import corpora_get_props_from_anndata
from backend.common.errors import PrepareError, DatasetAccessError, FilterError, UnsupportedSummaryMethod
from backend.common.errors import PrepareError, DatasetAccessError, FilterError
from backend.common.utils.type_conversion_utils import get_schema_type_hint_of_array
from backend.server.compute.scanpy import scanpy_umap
from backend.server.data_common.data_adaptor import DataAdaptor
@@ -69,11 +68,11 @@ class AnndataAdaptor(DataAdaptor):
@staticmethod
def _create_unique_column_name(df, col_name_prefix):
""" given the columns of a dataframe, and a name prefix, return a column name which
does not exist in the dataframe, AND which is prefixed by `prefix`
"""given the columns of a dataframe, and a name prefix, return a column name which
does not exist in the dataframe, AND which is prefixed by `prefix`
The approach is to append a numeric suffix, starting at zero and increasing by
one, until an unused name is found (eg, prefix_0, prefix_1, ...).
The approach is to append a numeric suffix, starting at zero and increasing by
one, until an unused name is found (eg, prefix_0, prefix_1, ...).
"""
suffix = 0
while f"{col_name_prefix}{suffix}" in df:
@@ -200,10 +199,10 @@ class AnndataAdaptor(DataAdaptor):
self.parameters.update({"diffexp_may_be_slow": True})
def _is_valid_layout(self, arr):
""" return True if this layout data is a valid array for front-end presentation:
* ndarray, dtype float/int/uint
* with shape (n_obs, >= 2)
* with all values finite or NaN (no +Inf or -Inf)
"""return True if this layout data is a valid array for front-end presentation:
* ndarray, dtype float/int/uint
* with shape (n_obs, >= 2)
* with all values finite or NaN (no +Inf or -Inf)
"""
is_valid = type(arr) == np.ndarray and arr.dtype.kind in "fiu"
is_valid = is_valid and arr.shape[0] == self.data.n_obs and arr.shape[1] >= 2
@@ -368,29 +367,3 @@ class AnndataAdaptor(DataAdaptor):
def get_var_keys(self):
# return list of keys
return self.data.var.keys().to_list()
def get_gene_set_summary(self, geneset_name, genes, method):
if method != "mean":
raise UnsupportedSummaryMethod("Unknown gene set summary method.")
var_index = self.parameters.get("var_names")
obs_selector, var_selector = self._filter_to_mask(
{
"var": {
"annotation_value": [
{
"name": var_index,
"values": genes,
}
]
}
}
)
X = self.get_X_array(obs_selector, var_selector)
if sparse.issparse(X):
mean = X.mean(axis=1)
else:
mean = X.mean(axis=1, keepdims=True)
col_idx = pd.Index([geneset_name])
return encode_matrix_fbs(mean, col_idx=col_idx, row_idx=None)