Notebook

Myeloid 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 Myeloid cells, this was done in two steps - all Myeloid cells, and a focused, iterative round of clustering to better identify Dendritic cell types.

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

In [2]:

in_files = [
    'c38df326-662d-459b-982d-0186c022f70d', # Myeloid Cell .h5ad
    '892e4fb0-8dad-4cb6-bcec-8f29b3dcd15e'  # Dendritic Cell .h5ad
]
hise_res = hisepy.reader.cache_files(in_files)

downloading fileID: c38df326-662d-459b-982d-0186c022f70d
downloading fileID: 892e4fb0-8dad-4cb6-bcec-8f29b3dcd15e
Files have been successfully downloaded!

In [3]:

out_files = [
    'annotations/pbmc_ref_myeloid_annotations_2024-02-29.csv',
    'annotations/pbmc_ref_myeloid-dcs_annotations_2024-02-29.csv'
]

In [4]:

study_space_uuid = '64097865-486d-43b3-8f94-74994e0a72e0'
title = 'Myeloid 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
)

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/04-Annotation/13-Python_Myeloid_cell_annotations.ipynb
3) /home/jupyter/scRNA-Reference-IH-A/version_adaptation/04-Python_adapt_T_cells.ipynb
Please select (1-3)

you are trying to upload file_ids... ['annotations/pbmc_ref_myeloid_annotations_2024-02-29.csv', 'annotations/pbmc_ref_myeloid-dcs_annotations_2024-02-29.csv']. Do you truly want to proceed?

Out[5]:

{'trace_id': '909f079b-9565-4579-bd59-58ebbbb66bb0',
 'files': ['annotations/pbmc_ref_myeloid_annotations_2024-02-29.csv',
  'annotations/pbmc_ref_myeloid-dcs_annotations_2024-02-29.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
anyio                       NA
arrow                       1.3.0
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comm                        0.1.4
cryptography                41.0.7
cycler                      0.10.0
cython_runtime              NA
dateutil                    2.8.2
db_dtypes                   1.1.1
debugpy                     1.8.0
decorator                   5.1.1
defusedxml                  0.7.1
deprecated                  1.2.14
exceptiongroup              1.2.0
executing                   2.0.1
fastjsonschema              NA
fqdn                        NA
google                      NA
greenlet                    2.0.2
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h5py                        3.10.0
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pytz                        2023.3.post1
referencing                 NA
requests                    2.31.0
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rfc3986_validator           0.1.1
rpds                        NA
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termcolor                   NA
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zmq                         25.1.2
zoneinfo                    NA

-----
IPython             8.19.0
jupyter_client      8.6.0
jupyter_core        5.6.1
jupyterlab          4.0.10
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 2024-02-29 22:24

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