insightsengineering / teal.modules.hermes

RNA-seq analysis modules to add to a teal application
https://insightsengineering.github.io/teal.modules.hermes/
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251 Add a getting started vignette #300

Closed BFalquet closed 1 year ago

BFalquet commented 1 year ago

https://github.com/insightsengineering/teal.modules.hermes/issues/251

close #251

move text from readme to vignette

thank you for the review

close #299

danielinteractive commented 1 year ago

Thanks @BFalquet ! Actually this goes well together with the fact that example in README is broken. We should better have the example in the vignette so that it is being run (if possible)

BFalquet commented 1 year ago

Thanks @BFalquet ! Actually this goes well together with the fact that example in README is broken. We should better have the example in the vignette so that it is being run (if possible)

Yes, good point, I also noticed that it was not working so I modified a bit the example, I should have mentioned it in the PR desecription.

github-actions[bot] commented 1 year ago

badge

Code Coverage Summary

Filename              Stmts    Miss  Cover    Missing
------------------  -------  ------  -------  -------------------------------------------------------------------------------------------------------------------------------
R/adtteSpec.R           156     113  27.56%   248-383
R/assaySpec.R            44      36  18.18%   103-142
R/barplot.R             169     136  19.53%   40-64, 123-259
R/boxplot.R             172     144  16.28%   41-65, 119-260
R/checkmate.R            18       9  50.00%   110-118
R/experimentSpec.R       89      56  37.08%   97, 215-282
R/forestplot.R          197     172  12.69%   60-91, 147-312
R/geneSpec.R            255     153  40.00%   153-168, 297-481
R/km.R                  189     158  16.40%   63-92, 153-307
R/pca.R                 355     272  23.38%   35-55, 163-464
R/quality.R             298     228  23.49%   18-109, 203-431
R/sampleVarSpec.R       232     103  55.60%   290, 309-315, 321-328, 330, 338-350, 352-353, 355, 358, 366-370, 372-387, 392-416, 419-423, 425, 432-442, 444-445, 453, 498-515
R/scatterplot.R         167     137  17.96%   40-64, 122-258
R/utils.R                16       5  68.75%   74-78
R/volcanoplot.R         193     163  15.54%   35-56, 111-280
R/zzz.R                   1       1  0.00%    2
TOTAL                  2551    1886  26.07%

Diff against main

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

Results for commit: f433cf940b0b8f02445cbd95c9f546b29a908693

Minimum allowed coverage is 80%

:recycle: This comment has been updated with latest results

github-actions[bot] commented 1 year ago

Unit Tests Summary

  1 files  15 suites   24s :stopwatch: 56 tests 34 :heavy_check_mark: 22 :zzz: 0 :x: 76 runs  54 :heavy_check_mark: 22 :zzz: 0 :x:

Results for commit 297048aa.

:recycle: This comment has been updated with latest results.