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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

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travis-m-blimkie
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@travis-m-blimkie
Merge pull request #23 from travis-m-blimkie/master
1cc56e2 
Updating devel branch to master
@travis-m-blimkie
Strip text size in tr_theme is now set relative to base_size argument.
f2ccda6
@travis-m-blimkie
Updated data objects and documentation.
d362d97
@travis-m-blimkie
Tweaks to main vignette.
2c20a41
@travis-m-blimkie
tr_qc_plots looks for an additional file for Phred scores.
14831c0
@travis-m-blimkie
Fixed missing file extension.
f103013
@travis-m-blimkie
Fixed code for reading alt phred score file.
2be58bb
@travis-m-blimkie
Streamlined tr_qc_plot code. Phred score data has consistent column o…
2432ff5 
…rder, sample names are trimmed of R1 suffix.
@travis-m-blimkie
Adjusted theme of qc plots.
612eb8d
@travis-m-blimkie
Added box plot option to tr_qc_plots, with toggleable points.
ba04582
@travis-m-blimkie
Added qc box plots to vignette. Tweaks to their theme.
6bb2082
@travis-m-blimkie
Small tweak to vignette.
c9ecf51
@travis-m-blimkie
Added an extra check and test to get_rounded_max.
6c67092
@travis-m-blimkie
Fixed version number. Tweaks to vignette.
f2c3e19
@travis-m-blimkie
Edits to tr_anno_cleaner code.
4c929a2
@travis-m-blimkie
Streamlined code in tr_clean_deseq2_result.
0ea8cea
@travis-m-blimkie
Specified default plot type in tr_qc_plots.
63a9296
@travis-m-blimkie
Streamlined code in tr_tidy_gage.
0276687
@travis-m-blimkie
Updated function docs.
29379b1
@travis-m-blimkie
Removed snaps from git tracking.
8d8143d
@travis-m-blimkie
tr_qc_plots now handles sample with R1 and/or R2. Tests added to supp…
3bbabd9 
…ort.
@travis-m-blimkie
Lowered Phred scores of one sample for testing. Added titles to qc_pl…
9fbbeb6 
…ots.
@travis-m-blimkie
qc plot type check is done at the beginning.
ff92392
@travis-m-blimkie
tr_qc_plots: When add_points is FALSE, show outliers with the same ae…
b1238e5 
…sthetics.
@travis-m-blimkie
tr_qc_plots: added options for customizing threshold line.
cc802a6
@travis-m-blimkie
tr_qc_plots: Fixed output assignment.
032724b
@travis-m-blimkie
Function in vignette to streamline code a bit.
f878f49
@travis-m-blimkie
tr_qc_plots: long x axis labels in box plots get wrapped.
eb0b9dc
@travis-m-blimkie
tr_qc_plots: Set seed for Phred plot labels. Removed qc column from o…
4a28d58 
…utput data.
@travis-m-blimkie
Updated some docs. Updated LICENSE via usethis to clear checks. Bumpe…
4cd4548 
…d version for release.
@travis-m-blimkie travis-m-blimkie merged commit 1f0286e into master Jun 24, 2024
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@travis-m-blimkie