Notebook

B cell annotations¶

In this notebook, we upload cell type annotations assigned by our domain experts. These annotations were generated using markers and by interactive investigation of our .h5ad files.

As these are derived from our .h5ad files, we'll connect them to the HISE analysis chain by chaching those files and using hisepy.upload.upload_files().

In [1]:

import hisepy
from datetime import date

For B cells, this was done in two steps - all B cells that were clustered after Immunoglobulin removal, and with subclustering of non-effector memory B cells.

Here, we'll combine these steps to build the link in our reproducibility chain.

In [2]:

in_files = [
    '99f83994-26ee-49af-a882-c1f2558daed2', # B cell .h5ad
    '51838754-b378-4f13-b447-82511bcd0a66'  # B Memory cell focus .h5ad
]
hise_res = hisepy.reader.cache_files(in_files)

downloading fileID: 99f83994-26ee-49af-a882-c1f2558daed2
downloading fileID: 51838754-b378-4f13-b447-82511bcd0a66
Files have been successfully downloaded!

In [3]:

out_files = [
    'annotations/pbmc_ref_b-cells-no-ig_annotations_2024-03-08.csv',
    'annotations/pbmc_ref_b-cells-mem-no-ig_annotations_2024-03-08.csv'
]

In [4]:

study_space_uuid = '64097865-486d-43b3-8f94-74994e0a72e0'
title = 'Ref. B cell annotations {d}'.format(d = date.today())

In [5]:

hisepy.upload.upload_files(
    files = out_files,
    study_space_id = study_space_uuid,
    title = title,
    input_file_ids = in_files
)

annotations/pbmc_ref_b-cells-no-ig_annotations_2024-03-08.csv
annotations/pbmc_ref_b-cells-mem-no-ig_annotations_2024-03-08.csv
Cannot determine the current notebook.
1) /home/jupyter/scRNA-Reference-IH-A/04-Annotation/12-Python_B_cell_annotations.ipynb
2) /home/jupyter/scRNA-Reference-IH-A/visualizations/04-Python_other_markers.ipynb
3) /home/jupyter/scRNA-Reference-IH-A/visualizations/03-Python_T_markers.ipynb
Please select (1-3)

you are trying to upload file_ids... ['annotations/pbmc_ref_b-cells-no-ig_annotations_2024-03-08.csv', 'annotations/pbmc_ref_b-cells-mem-no-ig_annotations_2024-03-08.csv']. Do you truly want to proceed?

Out[5]:

{'trace_id': '9dae5780-00b0-47c4-b148-ee2f2868bd9e',
 'files': ['annotations/pbmc_ref_b-cells-no-ig_annotations_2024-03-08.csv',
  'annotations/pbmc_ref_b-cells-mem-no-ig_annotations_2024-03-08.csv']}

In [6]:

import session_info
session_info.show()

Out[6]:

Click to view session information

-----
hisepy              0.3.0
session_info        1.0.0
-----

Click to view modules imported as dependencies

PIL                         10.0.1
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deprecated                  1.2.14
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fqdn                        NA
google                      NA
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requests                    2.31.0
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-----
IPython             8.19.0
jupyter_client      8.6.0
jupyter_core        5.6.1
jupyterlab          4.1.2
notebook            6.5.4
-----
Python 3.10.13 | packaged by conda-forge | (main, Dec 23 2023, 15:36:39) [GCC 12.3.0]
Linux-5.15.0-1052-gcp-x86_64-with-glibc2.31
-----
Session information updated at 2024-03-09 04:56

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