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R_code_revamp_sample_corr #449

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R_code_revamp_sample_corr #449

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PaulJonasJost
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Changed Sample Correlation Server:

  1. Removed unnecessary arguments in Server creation
  2. Removed unnecessary arguments as reactive values for counts and updating
  3. Changed calculation such that annotation changes do not trigger recalculation (had to change library from pheatmap away)
  4. Moved actual calculations needed for the plot

@PaulJonasJost
removed unused file
508fe91
@PaulJonasJost
first step: made data selection a function to outsource actualy proce…
1ea35cb 
…ssing. Done for future bulletproofing of R Code Snippets
@PaulJonasJost
Tmp commit
21f28b1
@PaulJonasJost
Merge branch 'develop' into R_code_revamp
196ac31
@PaulJonasJost
Moved all relevant functionality outside of base server. Will be used…
7546b33 
… for code creation Later!

Addtionally closes #447, Closes #435
And fixes a Small bug in the report where the batch formula and regular formula of deseq processing would be swapped
@PaulJonasJost
removed browser
5596bf8
@PaulJonasJost
unnecessary komma
259afec
@PaulJonasJost
Fixed a bug in picture download
bb134de
@PaulJonasJost
Changed Sample Correlation Server:
fb95061 
1. Removed unnecessary arguments in Server creation
2. Removed unnecessary arguments as reactive values for counts and updating
3. Changed calculation such that annotation changes do not trigger recalculation (had to change library from pheatmap away)
4. Moved actual calculations needed for the plot
@PaulJonasJost PaulJonasJost requested a review from LeaSeep February 1, 2025 13:55
@PaulJonasJost PaulJonasJost self-assigned this Feb 1, 2025
@PaulJonasJost PaulJonasJost added enhancement New feature or request ready for review labels Feb 1, 2025
@PaulJonasJost
Renamed Default Title Creation
996a3ff
@PaulJonasJost
Better handling as Boolean Value
23e85c6
@PaulJonasJost
For now: Split plotting and PCA calculation into two! -> both still u…
8349c3a 
…gly but now managable
@PaulJonasJost
Experimental: make the waiter a reactive value to turn it on/off in m…
c2921df 
…ultiple stages without always redefining it
@PaulJonasJost
Restructured computation code such that it is separated and actual fu…
9ae36e7 
…nctionality is outsourced
@PaulJonasJost
Restructured code such that each plot is rendering on its own. (Neede…
8938853 
…d for clearer code for plotting, used later in R code)
@PaulJonasJost
All code reworked in PCA, should be now easy to generate R Code.
9bcf7a2
@PaulJonasJost
removed unneccessary arguments for module
ffe0528
@PaulJonasJost
Downloading figure triggers report instead of full code. Also Report …
b55ebbb 
…independent of values generated in calculation.
@PaulJonasJost
Moved Report outside
cd173f7
Base automatically changed from R_code_revamp to develop February 4, 2025 08:23
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As discussed, I merged other parts of the codes into this already. (previous PRs)

@PaulJonasJost
Merge branch 'develop' into R_code_revamp_sample_corr
dffeaec 
# Conflicts:
#	program/shinyApp/R/pca/server.R
#	program/shinyApp/R/util.R
#	program/shinyApp/server.R
@PaulJonasJost
Removed unnecessary reactive value
34de036
PaulJonasJost and others added 10 commits February 5, 2025 18:09
@PaulJonasJost
Made the significance analysis one singular function
b3738f7
@PaulJonasJost
Merge branch 'develop' into R_code_revamp_sample_corr
083a7ac 
# Conflicts:
#	program/shinyApp/server.R
@PaulJonasJost
Merge branch 'R_code_revamp_sample_corr' into R_code_revamp_heatmap
49548a2
@PaulJonasJost
Moved functions where they belong to
75d6169
@PaulJonasJost
Moved Plot outside as it is already plotting a reactive value
4779e56
@PaulJonasJost
Intermediate: something with leas new thing is not working....
709a375
@PaulJonasJost
Separate Plotting function for upset withpout highlighting
3f4eff0
@PaulJonasJost
Separate plotting function for volcanos. Checked plot generation and …
e960a3f 
…reactivity. R Code ignored (as before)

Currently no separate code for highlighting download (should we change that?)
@PaulJonasJost
Slight name changes and corresponding par_tmp updates
9fb6c73
@PaulJonasJost
Merge pull request #454 from ICB-DCM/R_code_revamp_sig_ana
19a9c21 
R_code_revamp_sig_ana
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