Release 1.2.0 #504
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Release 1.2.0 #504
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* subtle changes to doc * indicate that batch collection is optional - addresses a bit #418 * adjust color of get buttons; parallelize format * slight changes, should close #413 * adding explocit helper file to batch correction, closes #418 * do the tip more obvious and change here to this page * closes #414 * making top links more obvious; no order change #415 * make cOmicsArt print prettier * make letters bold * changed to show debug text again; to let user know what is going on addresses #421 (#422)
Fixed link for Showcases in Video Tutorial
…ssing. Done for future bulletproofing of R Code Snippets
* Update README.md * Update README.md * Updates based on thorough first user assessment (#426) * changed to show debug text again; to let user know what is going on; addresses #421 * Make things clearer in layout, incl. button design, placement, tip highlights and promoting more parallelism (#419, #413, #414) * changes and clean up to the docs to easen the retrieval of information * indicate that batch collection is optional, adding explicit help file - addresses #418 * making top links more obvious; attention no order change #415 as suggested * make cOmicsArt print prettier * Crash fix sig ana (#420) * add hiding of tabs to avoid usage of results; fixes #417 * fixed to work with native SumExp next to cOmicsArt created #404 (#425) * Renamed SigAna to Diff Ana in docs * Renamed Sig ana to Diff ana within code * Changed Sig Ana to Diff ana also in hiding tabs etc * Also show tab again after preprocessing * Update docs/screen_recording.md Co-authored-by: Lea Seep <74967328+LeaSeep@users.noreply.github.com> --------- Co-authored-by: Lea Seep <74967328+LeaSeep@users.noreply.github.com>
* Moved optional tests to bottom * More clear Message for optional tests. How NAs are handled is mentioned in the specific cases.
* Update README.md * Update README.md * Updates based on thorough first user assessment (#426) * changed to show debug text again; to let user know what is going on; addresses #421 * Make things clearer in layout, incl. button design, placement, tip highlights and promoting more parallelism (#419, #413, #414) * changes and clean up to the docs to easen the retrieval of information * indicate that batch collection is optional, adding explicit help file - addresses #418 * making top links more obvious; attention no order change #415 as suggested * make cOmicsArt print prettier * Crash fix sig ana (#420) * add hiding of tabs to avoid usage of results; fixes #417 * fixed to work with native SumExp next to cOmicsArt created #404 (#425) * Removed legend from one plot * Adjusted so downloading should still work * Download now correctly working. Before: Download not working for anything aside from DESeq2 and DESeq2 not working on multi tabs * Due to the observe functionality, the info text was greyed out. adapted to other display functionalities * Readjusted layout a tiny bit (instead of stacking the options for change). Volcanos now shown on top of each other with legend toggable * Changes also for deseq2 * Fixed error that lead to wrong tab creation * Fixed error of deleting report events --------- Co-authored-by: Lea Seep <74967328+LeaSeep@users.noreply.github.com>
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
…gly but now managable
…ultiple stages without always redefining it
…nctionality is outsourced
…d for clearer code for plotting, used later in R code)
* removed unused file * first step: made data selection a function to outsource actualy processing. Done for future bulletproofing of R Code Snippets * Tmp commit * Moved all relevant functionality outside of base server. Will be used 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 * removed browser * unnecessary komma * We should remove this rather old info * Update program/shinyApp/R/util.R Co-authored-by: Lea Seep <74967328+LeaSeep@users.noreply.github.com> * non global assignment --------- Co-authored-by: Lea@Mac <leaseep@gmail.com> Co-authored-by: Lea Seep <74967328+LeaSeep@users.noreply.github.com>
…independent of values generated in calculation.
…wnload R Code (although completely wrong) creates a fast zip file
* adresses #478 * small UI update for more guidiance * added customMessages to actual clear the values * clearly notifys user upon data upload about state * add initital stauts with Pauls beloved conditionalPanel * adding explicit filenames to further guide user which was the latest uplaoded data * adding remove of tabs to further show clearance
* Notes fixed with additional option to put own notes * Able to push notes from textarea * Saving edited html
* start of adding addtional datasets * adding actual data * change apparent genes to entities * hide enrichment tab for all but Transcriptomics * add updated data * Fixed error preventing new upload * Fixed error showing/hiding tabs resulting in no rendering of summary * Fixed Problem of plots generating before they were allowed to in preprocessing * Fixed problems of updating plots with wrong data. Side effect: Clear all plots when uploading new data --------- Co-authored-by: PaulJonasJost <jost.pauljonas@gmail.com>
* csv updated * c.R update * add new rds --------- Co-authored-by: Lea@Mac <leaseep@gmail.com>
* Meand and SD plot * Adjusted notes * Explicitely add vsn as library * adding package that was revoking interactive selection * testing github * testing success --------- Co-authored-by: Lea@Mac <leaseep@gmail.com>
* Correct allow_plot placement * Removed warnings catcher, corrected x-axis
…. Also replaced report generation in plot saving with button click. Closes #498
* Fix Loadings plots * Fix problem in data selection due to wrong assignment * Clear plot in case of error * Removed constants in case of sub selection of data
# Conflicts: # program/shinyApp/R/pca/ui.R # program/shinyApp/R/pre_processing/ui.R # program/shinyApp/R/significance_analysis/ui.R # program/shinyApp/helpfiles/PreProcessing_Procedures.md # program/shinyApp/server.R
* Enable wilcoxon byproduct: fixing sd mean plot * Fixed bug where metabolomics data had no name
* Fixed bug where overrepresenation analysis file upload did not appear. This was because i took it over from the server side with an renderUI which is not meant to be in ui. closes #507 * fixed bug such that ORA actually working; added test data to also showcase structure --------- Co-authored-by: Lea@Mac <leaseep@gmail.com>
* mv dupl text to template string * old button is back as this fixes the bug #509 * fixing old vs new names being the same
* Temp: Data clearing trigger whole page reload. Changes only relevant in server.R * Reverted UI changes
* un-uncommented relevant part of the code * changed so it works with VI as well * add VI help --------- Co-authored-by: Lea@Mac <leaseep@gmail.com>
* FAQ update * adding quick link * update PCA on how to discover batches * VI details * rm dupliacted desing matrix info * extention pre-processing * add warning * make it prettier * Update docs/faq.md * grammar fixes by Paul
* Small bug in PCA code generation * R code rework * R code example * small bugfix * adjusted such that example matches figures
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