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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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Fix pca error #325

Closed gogonzo closed 1 year ago

gogonzo commented 1 year ago

suppose to fix #319

I found the origin of the error but I'm not sure how to fix it exactly. Reactivity of the module seems to be wrong. I tried to change start_col_data from eventReactive to reactive so that it react to change of the data also - error disappeared but it also caused optional color variable (sample var) to be deselected. So I think it'd be better if you @danielinteractive have try to fix it further. I've added a comment before the failing line

github-actions[bot] commented 1 year ago

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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       94      61  35.11%   97, 215-287
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%   291, 310-316, 322-329, 331, 339-351, 353-354, 359, 362, 370-374, 376-391, 396-420, 423-427, 429, 436-446, 448-449, 457, 502-519
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                  2556    1891  26.02%

Diff against main

Filename              Stmts    Miss  Cover
------------------  -------  ------  -------
R/experimentSpec.R       +5      +5  -1.97%
TOTAL                    +5      +5  -0.05%

Results for commit: 232448e8e7bca2f23edb1541ed817d6674c40653

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   10s :stopwatch: 56 tests 43 :heavy_check_mark: 13 :zzz: 0 :x: 85 runs  72 :heavy_check_mark: 13 :zzz: 0 :x:

Results for commit fabefee9.

danielinteractive commented 1 year ago

Thanks @gogonzo , @BFalquet can you take this on?

BFalquet commented 1 year ago

Thanks @gogonzo , @BFalquet can you take this on?

I think this is related to the bug i am currently fixing in #323 . I ll keep you posted.

BFalquet commented 1 year ago

Thanks @gogonzo , @BFalquet can you take this on?

I think this is related to the bug i am currently fixing in #323 . I ll keep you posted.

So the fix in https://github.com/insightsengineering/teal.modules.hermes/pull/326 seem to also solve the issue.

danielinteractive commented 1 year ago

not needed because it is solved in #326