update tests and docs

[gravesti]

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✅ All contributors have signed the CLA
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Unit Tests Summary

  1 files   23 suites   1m 3s ⏱️
273 tests 267 ✅ 6 💤 0 ❌
787 runs  781 ✅ 6 💤 0 ❌

Results for commit 8dc0f8a.

♻️ This comment has been updated with latest results.

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Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
differential	💔	$28.57$	$+9.54$	$0$	$0$	$+2$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
differential	💔	$0.69$	$+8.94$	autoplot_for_HermesDataDiffExpr_works_as_expected_with_default_options

Results for commit 12c3d1f

♻️ This comment has been updated with latest results.

[gravesti]

I have read the CLA Document and I hereby sign the CLA

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Code Coverage Summary

Filename                   Stmts    Miss  Cover    Missing
-----------------------  -------  ------  -------  ------------------------
R/assertthat.R                19       1  94.74%   149
R/calc_cor.R                  25       0  100.00%
R/checkmate.R                  4       0  100.00%
R/connections.R              143     125  12.59%   27-161, 215-287, 356-381
R/differential.R             101       3  97.03%   190, 193, 196
R/dplyr_compatibility.R        3       1  66.67%   23
R/draw_barplot.R              34       0  100.00%
R/draw_boxplot.R              71       5  92.96%   81, 88-89, 106, 109
R/draw_heatmap.R              35       1  97.14%   71
R/draw_scatterplot.R          32       4  87.50%   73-74, 87, 93
R/GeneSpec-class.R            68       0  100.00%
R/graphs.R                   107       3  97.20%   107-109
R/HermesData-class.R          35       4  88.57%   134-137
R/HermesData-methods.R       194       0  100.00%
R/HermesData-validate.R       44       0  100.00%
R/join_cdisc.R                37       0  100.00%
R/normalization.R            100       2  98.00%   194, 223
R/pca_cor_samplevar.R         59       0  100.00%
R/pca.R                       28       0  100.00%
R/quality.R                   75       3  96.00%   109-112
R/top_genes.R                 51       0  100.00%
R/utils.R                     98       0  100.00%
TOTAL                       1363     152  88.85%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  --------
TOTAL             0       0  +100.00%

Results for commit: 8dc0f8a

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[danielinteractive]

Thanks a lot @gravesti !

[gravesti]

@danielinteractive It looks like I hadn't pushed the latest changes from my side for the violin plot quantiles. From another package I know there will be a ggplot2 v4.0.0 release soon and this changes some arguments.
Basically, what I have above is kind of nonsense (but it is the change suggested is in the deprecation message).
It shouldn't give an error, but no quantiles will be plotted. I will prepare another PR for when ggplot2 4.0 is released.