ml and single cell utils.
Project description
ML and single cell analysis utils.
installation
pip install anutils
NOTE: To use anutils.scutils.sc_cuda, you need to install rapids first. see rapids.ai for details. For example, to install rapids on a linux machine with cuda 11, you can run:
pip install cudf-cu11 dask-cudf-cu11 --extra-index-url=https://pypi.nvidia.com
pip install cuml-cu11 --extra-index-url=https://pypi.nvidia.com
pip install cugraph-cu11 --extra-index-url=https://pypi.nvidia.com
usage
general utils: anutils.*
anutls.glimpse is similar to dplyr::glimpse in R, but enhanced in: - display the index - when passing show_unique=True, display the number of unique values for each column - when passing show_unique=True, display the unique values instead of the first N values for each column
import anutils as anu
df = pd.DataFrame({
'name': ['Alice', 'Bob', 'Carol', 'David', 'Eric'],
'letters': ['a', 'a', 'b', 'b', 'c'],
'digits': [1, 2, 3, 3, 3],
'colors': ['r', 'g', 'b', 'k', 'k'],
})
df.index = df['name']
anu.glimpse(df, show_unique=True)
# output:
# DataFrame: 5 rows, 4 columns
# index (name) <object> (5) ['Alice', 'Bob', 'Carol', 'David', 'Eric']
# $ name <object> (5) ['Alice', 'Bob', 'Carol', 'David', 'Eric']
# $ letters <object> (3) ['a', 'b', 'c']
# $ digits <int64> (3) [1, 2, 3]
# $ colors <object> (4) ['r', 'g', 'b', 'k']
single cell utils: anutils.scutils.*
plotting
from anutils import scutils as scu
# a series of embeddings grouped by disease status
scu.pl.embeddings(adata, basis='X_umap', groupby='disease_status', **kwargs) # kwargs for sc.pl.embedding
# enhanced dotplot with groups in hierarchical order
scu.pl.dotplot(adata, var_names, groupby, **kwargs) # kwargs for sc.pl.dotplot
cuda-accelerated scanpy functions
NOTE: to use these functions, you need to install rapids first. see installation for details.
from anutils.scutils import sc_cuda as cusc
# 10-100 times faster than `scanpy.tl.leiden`
cusc.sc.leiden(adata, resolution=0.5, key_added='leiden_0.5')
# 10-100 times faster than `scib.metrics.silhouette`
cusc.sb.silhouette(adata, group_key, embed)
machine learning utils:
import anutils.mlutils as ml
# to be added
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