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feat: Improve datavzrd tables #93

Merged
merged 109 commits into from
Aug 15, 2024
Merged

feat: Improve datavzrd tables #93

merged 109 commits into from
Aug 15, 2024

Commits on Apr 24, 2024

  1. Add initial changes

    Addimator committed Apr 24, 2024
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  2. First finished draft

    Addimator committed Apr 24, 2024
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Commits on May 24, 2024

  1. Improve datavzrd tables

    Addimator committed May 24, 2024
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  2. fix wrong paths

    Addimator committed May 24, 2024
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  3. fix wrong paths another time

    Addimator committed May 24, 2024
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Commits on Jun 5, 2024

  1. Add meta comparisons and tidy up

    Addimator committed Jun 5, 2024
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Commits on Jun 6, 2024

  1. Repair volcano plots

    Addimator committed Jun 6, 2024
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  2. Remove _se from confidence interval

    Addimator committed Jun 6, 2024
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Commits on Jun 7, 2024

  1. Update spia columns if no results produced

    Addimator committed Jun 7, 2024
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  2. Compute gene_ratio before selecting all columns

    Addimator committed Jun 7, 2024
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Commits on Jun 24, 2024

  1. Merge branch 'main' into locotact_p18

    @dlaehnemann
    dlaehnemann authored Jun 24, 2024
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  2. fix: remove accidental empty line in datavzrd.smk

    @dlaehnemann
    dlaehnemann authored Jun 24, 2024
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  3. fix: use lambda expression to get method wildcard into function argum… 

    …ent string
    @dlaehnemann
    dlaehnemann authored Jun 24, 2024
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  4. chore: make the formatter happy

    @dlaehnemann
    dlaehnemann authored Jun 24, 2024
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  5. chore: clean up unneeded workflow/scripts/postprocess_spia.py

    @dlaehnemann
    dlaehnemann authored Jun 24, 2024
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Commits on Jun 26, 2024

  1. Use yte in datavzrd

    Addimator committed Jun 26, 2024
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  2. Merge branch 'main' into locotact_p18

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    Addimator authored Jun 26, 2024
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Commits on Jun 27, 2024

  1. Merge branch 'main' into locotact_p18

    @johanneskoester
    johanneskoester authored Jun 27, 2024
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  2. Change display of q/pvals, remove NaN rows in diffexp

    Addimator committed Jun 27, 2024
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  3. Merge branch 'locotact_p18' of github.com:snakemake-workflows/rna-seq… 

    …-kallisto-sleuth into locotact_p18
    Addimator committed Jun 27, 2024
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  4. Update workflow/scripts/postprocess_diffexp.py 

    Co-authored-by: David Laehnemann <[email protected]>
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    Addimator and dlaehnemann authored Jun 27, 2024
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Commits on Jun 28, 2024

  1. Small fixes

    Addimator committed Jun 28, 2024
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  2. Merge branch 'locotact_p18' of github.com:snakemake-workflows/rna-seq… 

    …-kallisto-sleuth into locotact_p18
    Addimator committed Jun 28, 2024
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Commits on Jul 4, 2024

  1. fix: postprocess for all diffexp levels, use proper table for constra… 

    …ining matrix, sort in the right order
    @johanneskoester
    johanneskoester committed Jul 4, 2024
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  2. bump datavzrd

    @johanneskoester
    johanneskoester committed Jul 4, 2024
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Commits on Jul 5, 2024

  1. do not create pi-value sorting for genes-aggregated (no beta-values a… 

    …nd no pi-value)
    @johanneskoester
    johanneskoester committed Jul 5, 2024
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  2. fix arg

    @johanneskoester
    johanneskoester committed Jul 5, 2024
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Commits on Jul 8, 2024

  1. remove and put debugs

    Addimator committed Jul 8, 2024
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  2. Merge branch 'locotact_p18' of github.com:snakemake-workflows/rna-seq… 

    …-kallisto-sleuth into locotact_p18
    Addimator committed Jul 8, 2024
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  3. Ise pd.join instead of self-implementing it

    Addimator committed Jul 8, 2024
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  4. Fix merge of dfs

    Addimator committed Jul 8, 2024
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  5. sort diffexp bei signd_pi_val prefix only

    Addimator committed Jul 8, 2024
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Commits on Jul 9, 2024

  1. Change meta comparison description 

    Co-authored-by: David Laehnemann <[email protected]>
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    Addimator and dlaehnemann authored Jul 9, 2024
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  2. Chanke links between datavzrd views

    Addimator committed Jul 9, 2024
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  3. Merge branch 'locotact_p18' of github.com:snakemake-workflows/rna-seq… 

    …-kallisto-sleuth into locotact_p18
    Addimator committed Jul 9, 2024
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Commits on Jul 10, 2024

  1. Add meta comparisons

    Addimator committed Jul 10, 2024
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  2. bug fix for meta comps

    Addimator committed Jul 10, 2024
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  3. Improve description of meta comps in config

    Addimator committed Jul 10, 2024
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  4. Add meta comparisons to README

    Addimator committed Jul 10, 2024
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  5. Add meta_comparisons to CI config

    Addimator committed Jul 10, 2024
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Commits on Jul 11, 2024

  1. Add meta comparisons to three prime test config

    Addimator committed Jul 11, 2024
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Commits on Jul 12, 2024

  1. Make sort more intuitive

    Addimator committed Jul 12, 2024
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Commits on Jul 18, 2024

  1. Merge branch 'main' into locotact_p18

    @johanneskoester
    johanneskoester authored Jul 18, 2024
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  2. Cahnge path of meta_comp in config

    Addimator committed Jul 18, 2024
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  3. Merge branch 'locotact_p18' of github.com:snakemake-workflows/rna-seq… 

    …-kallisto-sleuth into locotact_p18
    Addimator committed Jul 18, 2024
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Commits on Jul 22, 2024

  1. Do own pca in order to allow scaling

    Addimator committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. change import of pca script

    Addimator committed Jul 23, 2024
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  2. make config setting for excluding nas in pca

    Addimator committed Jul 23, 2024
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  3. Sort tables and show sorting in description

    Addimator committed Jul 23, 2024
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  4. show scale in both plots in go meta comp

    Addimator committed Jul 23, 2024
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  5. Insert dealing with meta comp description

    Addimator committed Jul 23, 2024
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  6. Add samples.tsv in report

    Addimator committed Jul 23, 2024
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  7. Add linkouts to tables in meta_comp

    Addimator committed Jul 23, 2024
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  8. fix meta comp description

    Addimator committed Jul 23, 2024
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  9. Show inputs in report

    Addimator committed Jul 23, 2024
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  10. Show inputs in report 2

    Addimator committed Jul 23, 2024
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  11. Show signed_pi_val for diffexp

    Addimator committed Jul 23, 2024
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Commits on Jul 24, 2024

  1. Show input data in report

    Addimator committed Jul 24, 2024
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  2. Fix error in report

    Addimator committed Jul 24, 2024
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  3. Link genes and pathways ind meta comps

    Addimator committed Jul 24, 2024
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  4. Show scale on right plot of meta comp

    Addimator committed Jul 24, 2024
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  5. Merging on go enrichment wrong (quick fix)

    Addimator committed Jul 24, 2024
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Commits on Jul 31, 2024

  1. Add gene analysis for pathways

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Commits on Aug 1, 2024

  1. snakefmt does complains

    @Addimator
    Addimator authored Aug 1, 2024
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  2. Add pca_exclude_NA to test config

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    Addimator committed Aug 1, 2024
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  3. Merge branch 'locotact_p18' of https://github.com/snakemake-workflows… 

    …/rna-seq-kallisto-sleuth into locotact_p18
    @Addimator
    Addimator committed Aug 1, 2024
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  4. Add orgDb to test config

    @Addimator
    Addimator committed Aug 1, 2024
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  5. Add orgDB and pca_NA to other test config

    @Addimator
    Addimator committed Aug 1, 2024
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  6. remove units and samples datavzrd config because its too specific

    @Addimator
    Addimator committed Aug 1, 2024
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  7. Improve docu and typos

    @Addimator
    Addimator committed Aug 1, 2024
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  8. improve go enrichment postprocessing

    @Addimator
    Addimator committed Aug 1, 2024
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  9. Improve meta comparision config structure

    @Addimator
    Addimator committed Aug 1, 2024
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  10. minor go enrichment postprocessing bug fixes

    @Addimator
    Addimator committed Aug 1, 2024
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  11. improve readme

    @Addimator
    Addimator committed Aug 1, 2024
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  12. oops, redo samples and units

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    Addimator committed Aug 1, 2024
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  13. Make snakefmt happy

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Commits on Aug 2, 2024

  1. Change datavzrd colum to study items

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  2. Merge branch 'locotact_p18' of https://github.com/snakemake-workflows… 

    …/rna-seq-kallisto-sleuth into locotact_p18
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    Addimator committed Aug 2, 2024
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  3. Revert overwrite changes in three prime config

    @Addimator
    Addimator committed Aug 2, 2024
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  4. Improve config comments

    @Addimator
    Addimator authored Aug 2, 2024
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  5. Resolve problems with configs

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    Addimator committed Aug 2, 2024
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  6. Bug fixes

    Addimator committed Aug 2, 2024
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  7. Merge branch 'locotact_p18' of github.com:snakemake-workflows/rna-seq… 

    …-kallisto-sleuth into locotact_p18
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Commits on Aug 5, 2024

  1. Delete unnecessary file

    Addimator committed Aug 5, 2024
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  2. Typo

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  3. Small fixes in config

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  4. Improve descriptions

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Commits on Aug 9, 2024

  1. Refactor a lot of PR remarks

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  2. Give correct config path

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    Addimator authored Aug 9, 2024
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  3. Fix pca_exclude_NAs path

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  4. Merge branch 'locotact_p18' of https://github.com/snakemake-workflows… 

    …/rna-seq-kallisto-sleuth into locotact_p18
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    Addimator committed Aug 9, 2024
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  5. fix: datavzrd_input path

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Commits on Aug 12, 2024

  1. Change heading level of meta comparision in readme 

    Co-authored-by: David Laehnemann <[email protected]>
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    Addimator and dlaehnemann authored Aug 12, 2024
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  2. Make string easier to read 

    Co-authored-by: David Laehnemann <[email protected]>
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    Addimator and dlaehnemann authored Aug 12, 2024
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  3. fix species tin linkout

    Addimator committed Aug 12, 2024
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  4. remove a lot of unnecessary dependencies

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  5. Convert jupyter notebooks to python files

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  6. Merge branch 'locotact_p18' of https://github.com/snakemake-workflows… 

    …/rna-seq-kallisto-sleuth into locotact_p18
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  7. Include samples in workflow.rst

    Addimator committed Aug 12, 2024
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  8. Merge branch 'locotact_p18' of github.com:snakemake-workflows/rna-seq… 

    …-kallisto-sleuth into locotact_p18
    Addimator committed Aug 12, 2024
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  9. update for linting

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  10. Remove outcommented caption for linting

    Addimator committed Aug 12, 2024
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  11. Merge branch 'locotact_p18' of github.com:snakemake-workflows/rna-seq… 

    …-kallisto-sleuth into locotact_p18
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Commits on Aug 13, 2024

  1. Apply suggestions from code review 

    Apply Davids suggestions for better code quality

Co-authored-by: David Laehnemann <[email protected]>
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    Addimator and dlaehnemann authored Aug 13, 2024
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  2. fix get exclude_nas

    @Addimator
    Addimator committed Aug 13, 2024
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  3. remove unnecessary line

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Commits on Aug 15, 2024

  1. Merge branch 'main' into locotact_p18

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  2. fix typo 

    Co-authored-by: David Laehnemann <[email protected]>
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    Addimator and dlaehnemann authored Aug 15, 2024
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  3. improve descriptions 

    Co-authored-by: David Laehnemann <[email protected]>
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    Addimator and dlaehnemann authored Aug 15, 2024
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