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Find consistent way for checking for 'nan' in obs columns #8

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grst opened this issue Apr 9, 2020 · 7 comments
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Find consistent way for checking for 'nan' in obs columns #8

grst opened this issue Apr 9, 2020 · 7 comments
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grst commented Apr 9, 2020

In GitLab by @grst on Jan 19, 2020, 17:40

adata.obs columns are converted to categorical on plotting. None, NaN might be turned into str(nan) in that case which breaks pd.isna etc.
@grst grst self-assigned this Apr 9, 2020
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grst commented Apr 9, 2020

In GitLab by @grst on Jan 29, 2020, 10:08

call AnnData._sanitize right after reading. Then all nans will be consistently converted into strings.
This is, however, subject to change in the future and being discussed here: scverse/anndata#141

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grst commented Apr 9, 2020

In GitLab by @grst on Jan 30, 2020, 09:43

mentioned in commit b397c559de059b35742ec472564b7a01eaf060f1

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grst commented Apr 9, 2020

In GitLab by @grst on Jan 30, 2020, 10:27

closed via merge request !3

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grst commented Apr 9, 2020

In GitLab by @grst on Jan 30, 2020, 10:27

closed via commit b397c559de059b35742ec472564b7a01eaf060f1

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grst commented Apr 9, 2020

In GitLab by @grst on Jan 30, 2020, 10:27

mentioned in commit 8b2d20c55bb100f1f8a9e5df66dcd49706ce4f33

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grst commented Apr 9, 2020

In GitLab by @grst on Jan 30, 2020, 13:13

mentioned in commit 45f6698

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grst commented Apr 9, 2020

In GitLab by @grst on Jan 30, 2020, 13:13

mentioned in commit 4c565a1

@grst grst closed this as completed Apr 9, 2020
grst added a commit that referenced this issue Aug 23, 2020
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Sanitize imported data into column format.
2c049ef 
Fixes #6.
Fixes #8.
grst added a commit that referenced this issue Aug 23, 2020
@grst
Merge branch 'feat/parsers' into 'master'
ffc8ace 
Implement 10x and Tracer parser

Closes #6 and #8

See merge request icbi-lab/pipelines/singlecell_tcr!3
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