Get git hub pages #200
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Merge main into develop
* hot fix * load tidyr package for gather fucntion
* Fix gather again (#76) * hot fix * load tidyr package for gather fucntion * fixed data Upload bug; added data upload name check NEEDS to be in main! * removed forgotten browser statment Co-authored-by: Paul Jonas Jost <[email protected]> Co-authored-by: Paul Jonas Jost <[email protected]>
Co-authored-by: Lea Seep <[email protected]>
Fix overwriting of choices
* fixed PCA bug due to duplicated naming somehow * remove useShinyAlert as not necassary anymore referencing startUp message * updated renv (rudimentary checking - no obvious problems) * add version tracker to Report, draft idea of text snippets to report * fixed aestethics report * adjusting citation style * exchange 'selectInput' with 'virtualSelectInput' for speed purposes * futer 'virtualSelectInput' replacements for speed and search options * Update program/shinyApp/R/Report_text_snippets.R Co-authored-by: Paul Jonas Jost <[email protected]> * Update program/shinyApp/R/pca/server.R Co-authored-by: Paul Jonas Jost <[email protected]> * Update program/shinyApp/R/pca/ui.R Co-authored-by: Paul Jonas Jost <[email protected]> Co-authored-by: Paul Jonas Jost <[email protected]>
* Changes to ea. * Correct scenario assignment in ea. Also correct handling of modal pop-up
* Start of Significance analysis. Basic skeleton done. Needs fleshing out now. Also: Removal of unused tabs. * Working significance Analysis for DESeq. * Significance Analysis with visualization. * * Analysis info display * Automatic plot update * DESeq picture * add additional packages - seemingly a lot as updatet in `convience_fixes`. If this causes issues we can revert this and first merge then update lock.file * Added some minor fixes. * Saving of venn diagramm. * Reporting works manually. * Recreate Code for plot. * Picture saving reporting done. * Significance Analysis working for now. Co-authored-by: Lea@Mac <[email protected]>
* Updated CHANGELOG.md * Updated DESCRIPTION * specify namespace * load additional package; specificy namespace * adjusted lock.file * Catch a problem if there a no significant values in changelog Co-authored-by: Lea@Mac <[email protected]>
* Fix gather again (#76) * hot fix * load tidyr package for gather fucntion * fixed data Upload bug; added data upload name check NEEDS to be in main! * removed forgotten browser statment Co-authored-by: Paul Jonas Jost <[email protected]> Co-authored-by: Lea Seep <[email protected]>
# Conflicts: # program/shinyApp/ui.R
* uploaded first test * outsource sourcing * add gitworkflows for testing; adj. .gitignore * Update to only be triggered on pull_request * change the yaml * change workflow * correct syntax * changed master to v2 * correct lock file location * removed unnecassary party * explicitly load `jsonlite` * correct file path * test without system dependencies * add the init of biconductor for renv * changed renv calling * add RPSM package manager potentially solves Biconductor issue; add cache option * remove the init * update Renv.locl * try other renv * add missing packages * force install stringr * trty something again * downgrade stringr and hope for the best * change repos for troublesome packages * update_with less info * corrected syntax * correct syntax * os system change * syyntaaxxx * syntaxxa * make paragraph * come on * idk * idk * ahhhhh * idk * are you serious * i have no clue * :( * I want that this works * important for hasing * is it really ubuntu version * was RSQlite new version an issue * maybe pre installing * remove troublesome packages for now to see if we can come trough * trying again * add renv activate and see what happens * without renv lockfile * add specific location of lockfile * exclude `qvalue`-package which seems to be an isse but has dependencies.. * added renv cellar pacakges; packages that do not work on test remote * tryout new yaml file * add qvalue to beginning yaml * syntax * typoo * add status show * add updated packages * manually install shiny * last try * syntaxx * do restore with lock file * coreect location * maybe wreid `connectionObserver` issue * upgrade log file with new bioconductor version * try to catch XML file * syntax * remove qvalue from cellar and hope it finds reshape2 dependency now * remove unnecassary;stringr still issue * allow to move on even if not all packages are loaded _does this work * add enrichplot to cellar * add explicit system dependencies for igraph * syntaxa * get rid of unnecassary stuff * change folder structure for sections of tests * add changed files within test infrastructure * inserting cache option * test summarising steps * revert * changed to version 2 check if there is still a warning * bit more cleaning * important for caching * test out badges * remove unneassary notes * Update README.md * add captions * check if second job is capable to get cache * removed cellar and updated lock file * Second test and third test (#95) * significance analysis test and small bug fixes. * significance analysis test * test translate_ea * test check_annotation_enrichment_analysis * Adhere folder structure of tests. Added tests to pipeline. * revert back to original sourcing. Co-authored-by: Lea@Mac <[email protected]> Co-authored-by: PaulJonasJost <[email protected]> Co-authored-by: Paul Jonas Jost <[email protected]>
* removed assignment as the return value is questionable. * Moved some things to constant for better readability. * Removed ornaism as a choice as we chose it before already. * Update program/shinyApp/R/enrichment_analysis/server.R Co-authored-by: Lea Seep <[email protected]> --------- Co-authored-by: Lea Seep <[email protected]>
* Removed assignments, as return is questionable. * Removed comments, removed global variance dependency. * Mainly spacing and replacing = with =
* Removed assignment. Fixed typo * Replaced paste with paste0, removed comments, spacing. Removed updates from call, as i did not see any functionality anymore. * Reverted wrong change. * Corrected weird comma placement. * Better variable name for pca file.
* Remove assignment * removed update from function, some spacing. Moved color assignment to a function * added small docstring to function * Update program/shinyApp/R/sample_correlation/server.R Co-authored-by: Lea Seep <[email protected]> --------- Co-authored-by: Lea Seep <[email protected]>
* Removed unhelpful comments * Removed updates as parameter * Removed some print statements. Made significance_tabs_to_delete into a reactive value. * changed sig_result inot reactive instead of global variable. * Removed a warning my pycharm.
* Removed assignment. * Some cleanup. Nothing in particaular. * Small change.
* snippet_dataInput, default parameters last. * Updated Guide to reflect name change in app. * Deleted unused function + file * small spacing changes to save_pheatmap * moved save_pheatmap to utility functions * spacing in fun_readInSampleTable.R. Should we move to util as well? * Removed unused modal. * LogIt function, removed comments and print that were not helpful * Corrected to the intended getLFC function. Currently have two, definitely need to select only one. * Weird naming corrected. Spacing corrected * Removed FLAG_TEST_DATA_SELECTED from global constants as 1. it is not handled as a constant, 2. there is a local overwrite
* UI cleanup. * Removed unused security * removed assignment * Made Jokes a global variable. Tidied up data inspection * Moved preprocessing away. Made some if/else statments clearer. TODO: "addWarning" seems quite unintuitive right now * Apply suggestions from code review Co-authored-by: Lea Seep <[email protected]> * Moved getCurrentVersion to util --------- Co-authored-by: Lea Seep <[email protected]>
* tryCatch for Heatmaps * tryCatch for PCA * Added stop() function * Replaced stop() with return(NULL) * No additional tryCatch neccessary. Some cleanup, as updating did not work * tryCatch around sig ana. * Update program/shinyApp/R/util.R Co-authored-by: Lea Seep <[email protected]> * Linked github repo for issues * removed advanced deseq formula, as no support currently exists * Merge problems with omics_type vs omicsType --------- Co-authored-by: Lea Seep <[email protected]>
* tryCatch for Heatmaps * tryCatch for PCA * Added stop() function * Replaced stop() with return(NULL) * No additional tryCatch neccessary. Some cleanup, as updating did not work * tryCatch around sig ana. * UI cleanup. * Removed unused security * removed assignment * Made Jokes a global variable. Tidied up data inspection * Moved preprocessing away. Made some if/else statments clearer. TODO: "addWarning" seems quite unintuitive right now * Added tryExcept for preprocessing. * Fixed DESeq problem. Integrated suggestions
* Make helpmarks visible completely * Moved helper for Intersections correctly * Update program/shinyApp/R/significance_analysis/ui.R
* CHanged every button (except for Data Upload) to "Get $PanelName" * Added Line to EA sidebar
* First draft of the new outlay * Wrap RDS download in an id, to hide it. * - Hide RDS. - TryCatch around summarized experiment - Removed the toast, as it was always shown, even when upload failed. * Main panel hidden till first sucessfull data upload -> Problems with debugging!! Adde helper files
* replaced code snippet function * add sample Correlation correct code snippet * added PCA complete Code Snippets * code download heatmap and singleGene * add plots for sig analysis (UpSet and Venn) * Volcano Code Snippets added * delted old volcano * typo fix * overrepresentation download snippet * actually select data based on selection specifications --------- Co-authored-by: PaulJonasJost <[email protected]>
testing out
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mistake - wanted to merge to develop not main..... |
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deployment should now also work for develop branch