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Merge Devel to 1.4 #24

Merged
merged 30 commits into from
Jun 24, 2024
Merged

Merge Devel to 1.4 #24

merged 30 commits into from
Jun 24, 2024

Commits on Apr 18, 2024

  1. Merge pull request #23 from travis-m-blimkie/master 

    Updating devel branch to master
    @travis-m-blimkie
    travis-m-blimkie authored Apr 18, 2024
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  2. Strip text size in tr_theme is now set relative to base_size argument.

    @travis-m-blimkie
    travis-m-blimkie committed Apr 18, 2024
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Commits on Apr 25, 2024

  1. Updated data objects and documentation.

    @travis-m-blimkie
    travis-m-blimkie committed Apr 25, 2024
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  2. Tweaks to main vignette.

    @travis-m-blimkie
    travis-m-blimkie committed Apr 25, 2024
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Commits on Apr 29, 2024

  1. tr_qc_plots looks for an additional file for Phred scores.

    @travis-m-blimkie
    travis-m-blimkie committed Apr 29, 2024
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  2. Fixed missing file extension.

    @travis-m-blimkie
    travis-m-blimkie committed Apr 29, 2024
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  3. Fixed code for reading alt phred score file.

    @travis-m-blimkie
    travis-m-blimkie committed Apr 29, 2024
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  4. Streamlined tr_qc_plot code. Phred score data has consistent column o… 

    …rder, sample names are trimmed of R1 suffix.
    @travis-m-blimkie
    travis-m-blimkie committed Apr 29, 2024
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  5. Adjusted theme of qc plots.

    @travis-m-blimkie
    travis-m-blimkie committed Apr 29, 2024
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  6. Added box plot option to tr_qc_plots, with toggleable points.

    @travis-m-blimkie
    travis-m-blimkie committed Apr 29, 2024
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  7. Added qc box plots to vignette. Tweaks to their theme.

    @travis-m-blimkie
    travis-m-blimkie committed Apr 29, 2024
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Commits on May 13, 2024

  1. Small tweak to vignette.

    @travis-m-blimkie
    travis-m-blimkie committed May 13, 2024
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Commits on Jun 4, 2024

  1. Added an extra check and test to get_rounded_max.

    @travis-m-blimkie
    travis-m-blimkie committed Jun 4, 2024
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Commits on Jun 5, 2024

  1. Fixed version number. Tweaks to vignette.

    @travis-m-blimkie
    travis-m-blimkie committed Jun 5, 2024
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Commits on Jun 10, 2024

  1. Edits to tr_anno_cleaner code.

    @travis-m-blimkie
    travis-m-blimkie committed Jun 10, 2024
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  2. Streamlined code in tr_clean_deseq2_result.

    @travis-m-blimkie
    travis-m-blimkie committed Jun 10, 2024
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  3. Specified default plot type in tr_qc_plots.

    @travis-m-blimkie
    travis-m-blimkie committed Jun 10, 2024
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  4. Streamlined code in tr_tidy_gage.

    @travis-m-blimkie
    travis-m-blimkie committed Jun 10, 2024
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  5. Updated function docs.

    @travis-m-blimkie
    travis-m-blimkie committed Jun 10, 2024
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Commits on Jun 12, 2024

  1. Removed snaps from git tracking.

    @travis-m-blimkie
    travis-m-blimkie committed Jun 12, 2024
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  2. tr_qc_plots now handles sample with R1 and/or R2. Tests added to supp… 

    …ort.
    @travis-m-blimkie
    travis-m-blimkie committed Jun 12, 2024
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Commits on Jun 13, 2024

  1. Lowered Phred scores of one sample for testing. Added titles to qc_pl… 

    …ots.
    @travis-m-blimkie
    travis-m-blimkie committed Jun 13, 2024
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  2. qc plot type check is done at the beginning.

    @travis-m-blimkie
    travis-m-blimkie committed Jun 13, 2024
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  3. tr_qc_plots: When add_points is FALSE, show outliers with the same ae… 

    …sthetics.
    @travis-m-blimkie
    travis-m-blimkie committed Jun 13, 2024
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  4. tr_qc_plots: added options for customizing threshold line.

    @travis-m-blimkie
    travis-m-blimkie committed Jun 13, 2024
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  5. tr_qc_plots: Fixed output assignment.

    @travis-m-blimkie
    travis-m-blimkie committed Jun 13, 2024
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  6. Function in vignette to streamline code a bit.

    @travis-m-blimkie
    travis-m-blimkie committed Jun 13, 2024
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  7. tr_qc_plots: long x axis labels in box plots get wrapped.

    @travis-m-blimkie
    travis-m-blimkie committed Jun 13, 2024
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Commits on Jun 19, 2024

  1. tr_qc_plots: Set seed for Phred plot labels. Removed qc column from o… 

    …utput data.
    @travis-m-blimkie
    travis-m-blimkie committed Jun 19, 2024
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Commits on Jun 24, 2024

  1. Updated some docs. Updated LICENSE via usethis to clear checks. Bumpe… 

    …d version for release.
    @travis-m-blimkie
    travis-m-blimkie committed Jun 24, 2024
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