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fix_test_data #442

Merged
merged 9 commits into from
Feb 5, 2025
Merged

fix_test_data #442

merged 9 commits into from
Feb 5, 2025

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PaulJonasJost
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Found an Error in the Data that was responsible for the count matrix warning.

As far as i can see, the other warning comes from the annotation that has not been 100%. Workaround could be:

  • to only have ENS genes (downside: no annotation anymore)
  • To remove all NA columns (not nice, but i would guess that we already threw everything out that was not mappable from entrez to ENS in the very first place as GEO data is with ENTREZ)
  • just leave the NA be (in which case we need to answer the reviewer on this)
  • Hghlight more optional things!

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If I Upload the test data (after download) click visual inspection and use data it crashes
Is this why you opened #441 ? You assigned me - happy to do it but would do it on this branch, ok?

Also as mentioned in #428 we wanted to clear up intention - aka it should still have the warning, pass VI and be able to be used, correct?

Error for reference:

[1] "Data Input done"
Warning in file(file, "rt") :
  cannot open file 'www/8bdaf581f94c56c8cb21dee6139ab25f/updatedMatrix.csv': No such file or directory
Warning: Error in file: cannot open the connection
  100: file
   99: read.table
   98: read.csv
   97: read_file [R/util.R#74]
   96: eventReactiveValueFunc [/Users/lea/sciebo/Home/current/projects/HighSalt/program/shinyApp/server.R#1163]
   52: data_input_shiny
   45: observe [/Users/lea/sciebo/Home/current/projects/HighSalt/program/shinyApp/server.R#463]
   44: <observer>
    1: runApp

@PaulJonasJost
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If I Upload the test data (after download) click visual inspection and use data it crashes Is this why you opened #441 ? You assigned me - happy to do it but would do it on this branch, ok?

Yes, that's why I assigned you. You can do it on this branch 👍🏼

Also as mentioned in #428 we wanted to clear up intention - aka it should still have the warning, pass VI and be able to be used, correct?

Yes 👍🏼 I think the intention is mostly cleared up with the Optional/required tests, thus use data needs to adjust to that, I guess.

@LeaSeep
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LeaSeep commented Feb 3, 2025

Now: If passedVI is True, data from upload directly taken, if passedVI wrong - pop up error triggered, use data triggers the same error, If passedVI is turned from treu to false with our internal adjusmtents new variable changedDuringVI is set to true and changed data is used

@LeaSeep
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LeaSeep commented Feb 3, 2025

(not on purpose on this branch but should not harm)..Sorry
-added stars based on padj level (depending on user-sig ana level as well)
-added color gradient to LFC (low and high correpsonding to Volcano)
-added color gradient to padj and pvalue (gold to white - all white if > then user threshold
-hide multiple columns for declutter able to select/deselect chosen columns

  • disallow filterig for 'stars' as filter gave raw HTML code as categories -looked ugly

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Error when using test data -> Inspect data -> Use Data -> No Preprocessing -> Sig Ana (default values of cell). Error message

This is caused by either one of the mean values being 0 or by NAs in the testing.Warning: Error in seq.default: 'from' must be a finite number
86: stop
85: seq.default
83: create_new_tab_manual [R/significance_analysis/util.R#209]
82: create_new_tab [R/significance_analysis/util.R#27]
81: observe [R/significance_analysis/server.R#334]
80: observer:observeEvent(sig_ana_reactive$start_analysis)
1: shiny::runApp
The directory has been successfully removed.

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Otherwise works fine (would not review code in depth as i will probably work on it soon anyways

Two small remarks that are minor ones (perhaps not even needed):

  1. Default name of the csv file by download is now "csv.csv"
  2. Downloads the sig_level column in the csv but it is empty

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NOTE - we now changed the test data matrix having no NA

@LeaSeep LeaSeep merged commit a36e58c into develop Feb 5, 2025
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@PaulJonasJost PaulJonasJost deleted the fix_test_data branch February 5, 2025 16:17
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2 participants