scirpy.datasets.wu2020_3k

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scirpy.datasets.wu2020_3k#

scirpy.datasets.wu2020_3k()#

Return the dataset from [WMdA+20] as AnnData object, downsampled to 3000 TCR-containing cells. :rtype: MuData

Note

Scirpy example datasets are managed through Pooch.

By default, the dataset will be downloaded into your operating system’s default cache directory (See pooch.os_cache() for more details). If it has already been downloaded, it will be retrieved from the cache.

You can override the default cache dir by setting the SCIRPY_DATA_DIR environment variable to a path of your preference.

This is how the dataset was processed:

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import muon as mu
import pandas as pd

# Use this list of 3k barcodes for consistency with previous versions
barcodes = pd.read_csv("./3k_barcodes.csv", header=None)[0].values

barcodes = pd.Series(barcodes).str.replace("-\\d+$", "", regex=True).values

mdata = mu.read_h5mu("wu2020.h5mu")

assert mdata.obs_names.is_unique

mdata = mdata[barcodes, :].copy()

mdata

mdata.write_h5mu("wu2020_3k.h5mu", compression="lzf")
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