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feat: sort datavzrd tables #115

Merged
merged 120 commits into from
Sep 19, 2024
Merged

feat: sort datavzrd tables #115

merged 120 commits into from
Sep 19, 2024

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Addimator
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In this pull request we

  • Introduce pi_value scores for all meta_comparisions, go_enrichment, diffexp and pathways
  • Sort the tables according to their pi_value
  • Show datapoints in the meta comparisions where only one model has values
  • Improve table descriptions
  • Improve lazy df use in polars
  • Small bug fixes

Addimator and others added 30 commits April 24, 2024 09:19
Add initial changes
2f5322e
First finished draft
675126d
Improve datavzrd tables
35aefde
fix wrong paths
1ff92de
fix wrong paths another time
e96e3c8
Add meta comparisons and tidy up
d150643
Repair volcano plots
f87548b
Remove _se from confidence interval
406af87
Update spia columns if no results produced
b4ba7dd
Compute gene_ratio before selecting all columns
50806cb
@dlaehnemann
Merge branch 'main' into locotact_p18
ddcf4db
@dlaehnemann
fix: remove accidental empty line in datavzrd.smk
c505482
@dlaehnemann
fix: use lambda expression to get method wildcard into function argum…
fad56f3 
…ent string
@dlaehnemann
chore: make the formatter happy
0fb709a
@dlaehnemann
chore: clean up unneeded workflow/scripts/postprocess_spia.py
b2f9ae8
Use yte in datavzrd
a9dda2f
@Addimator
Merge branch 'main' into locotact_p18
cfb2b85
@johanneskoester
Merge branch 'main' into locotact_p18
cc97b93
Change display of q/pvals, remove NaN rows in diffexp
b3333f8
Merge branch 'locotact_p18' of github.com:snakemake-workflows/rna-seq…
c9ddbbe 
…-kallisto-sleuth into locotact_p18
@Addimator @dlaehnemann
Update workflow/scripts/postprocess_diffexp.py
69085eb 
Co-authored-by: David Laehnemann <[email protected]>
Small fixes
e3574c1
Merge branch 'locotact_p18' of github.com:snakemake-workflows/rna-seq…
76fc2bf 
…-kallisto-sleuth into locotact_p18
@johanneskoester
fix: postprocess for all diffexp levels, use proper table for constra…
d41b94a 
…ining matrix, sort in the right order
@johanneskoester
bump datavzrd
354aaac
@johanneskoester
do not create pi-value sorting for genes-aggregated (no beta-values a…
e0d4b76 
…nd no pi-value)
@johanneskoester
fix arg
baac24e
remove and put debugs
f6cc352
Merge branch 'locotact_p18' of github.com:snakemake-workflows/rna-seq…
0e56286 
…-kallisto-sleuth into locotact_p18
Ise pd.join instead of self-implementing it
2162866
Addimator and others added 25 commits August 12, 2024 09:48
@Addimator
remove a lot of unnecessary dependencies
004d2ee
@Addimator
Convert jupyter notebooks to python files
17f9711
@Addimator
Merge branch 'locotact_p18' of https://github.com/snakemake-workflows…
69e7e07 
…/rna-seq-kallisto-sleuth into locotact_p18
Include samples in workflow.rst
301204e
Merge branch 'locotact_p18' of github.com:snakemake-workflows/rna-seq…
b317173 
…-kallisto-sleuth into locotact_p18
@Addimator
update for linting
244c861
Remove outcommented caption for linting
1eea5b6
Merge branch 'locotact_p18' of github.com:snakemake-workflows/rna-seq…
055c4ee 
…-kallisto-sleuth into locotact_p18
@Addimator @dlaehnemann
Apply suggestions from code review
f60bf62 
Apply Davids suggestions for better code quality

Co-authored-by: David Laehnemann <[email protected]>
@Addimator
fix get exclude_nas
c4a63b3
@Addimator
remove unnecessary line
c827a9d
@Addimator
Introduce and sort with pi-signed-values
8b2d3ff
@Addimator
Bug fix nested data in enrichment preprocessing
755cd7f
Bug fixes
27d5f0b
Small fixes
fd75223
Change xplicit col names to regex
dec0a04
Improve table description
3cdffcb
Delete unncessary plot stuff
badec9d
Show partly missing values in meta comparision
47fe424
Merge branch 'main' into sort-datavzrd-tables
2a550b7
Tidy up
693756e
Fex meta comparision paths and hide text in plot
743cf72
fix meta comp paths
35cbdcc
Merge branch 'main' into sort-datavzrd-tables
8bf1b70
@Addimator
Correct formatting
f4f90f0
@johanneskoester johanneskoester merged commit 1ccc3fa into main Sep 19, 2024
5 checks passed
@johanneskoester johanneskoester deleted the sort-datavzrd-tables branch September 19, 2024 10:15
@github-actions github-actions bot mentioned this pull request Sep 19, 2024
Merged
johanneskoester pushed a commit that referenced this pull request Sep 20, 2024
@github-actions
chore(main): release 2.8.0 (#116)
74fda32 
🤖 I have created a release *beep* *boop*
---


##
[2.8.0](v2.7.2...v2.8.0)
(2024-09-20)


### Features

* sort datavzrd tables
([#115](#115))
([1ccc3fa](1ccc3fa))


### Bug Fixes

* Move signed_pi_value columns to the end (again)
([#117](#117))
([ac4a73b](ac4a73b))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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@Addimator @johanneskoester @dlaehnemann