"New Mini Release" #406
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"New Mini Release" #406
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* Add option whether to scale data to unit variance * Added it to downloadable code * Fixed small error regarding rds vs RDS files in code
* add Log2 as preprocessing * Added lines to help files and report output
* Fixed scaling and positioning of loading comic * Removed ID from each waiter class, across all pre-processing tabs. Single-gene visualization did not have a waiter class. --------- Co-authored-by: PaulJonasJost <[email protected]>
* add waiters show/hide to all R Code Download
* added explicit waiter; tried as reactive with waiter <- reactive({Waiter$new}) and then waiter()$show - did not work
…ix the broken image.
* introducing guide for small tutorial * pretty Welcome page * add question mark explanation to help; increase size and color of question marks * links now in question marks to precise location in docs * ensure people find the search bar in documentation * explicit mention package * Is the initial start of guide the issue of test failure * reverted - did not help * changed workflow file to retrieve reportet error * missing loading of cicerone in C the issue? * crispy up the guide * more crispy * add helptab ui... * Apply suggestions to code. --------- Co-authored-by: PaulJonasJost <[email protected]>
* background not see through, but loading comic still on top * adding distinct and clear message if connection is lost; addresses one to do in #357 * Refresh button plus issue opener and email contact --------- Co-authored-by: PaulJonasJost <[email protected]>
* hide by elemtn pre-processing options * Info box streamline (#370) * move info box data selection up * rm show independent of main panel * rm unnecassray helptext to be streamlined * moved all boxes and introduced where missing * fix crash within PCA when low numbers of entities selected; unsure if this was full rank error #357 * add heatmap message; fix bug when only one entitie selected * add info box to singel gene viz * adding default info, adressed #355 * Proof of concept, introducing div, to inititall hide and shoe upon button click * add divs to hide * PCA div added * fix bug to show within modules * seems to work, but EA buggy; need to investigate if show/hide the issue * bug fix in enrichment analysis, somehow had problem if no enrichment found, but result object created * finally also see enrichment default message * also now adjumstent for geneannotation - fixes #353 * Integrated suggested changes --------- Co-authored-by: PaulJonasJost <[email protected]>
* Get Rid of "MainFactor" inDEseq2 analysis * Update Questionmark helper
* Data Selection is "Optional" * propose to put buttons under each other and change color, as before they seemt to be on the same level * Merged develop and adjusted design --------- Co-authored-by: Lea@Mac <[email protected]>
… set was not working if we did not create seleted data before (#376)
* Fixed order of navigation in interface details. Added navigation within each page, moved video tutorial to the top and added link to showcases. Only pushing markdown files. Closes #359 * Apply suggestions from code review Co-authored-by: Lea Seep <[email protected]> --------- Co-authored-by: Lea Seep <[email protected]>
* added info about test data, as well as cied resources * moved text to C.R; did not do conditional panel - would merge anyway
…e waiter persisted. Just to be safe, waiter is now hidden whenever error modals show up. (#394)
* cookie tracks first visti; option to delete cookie * lets now user actively set cookie (seems to be EU-law) solves #364 * Update program/shinyApp/server.R Co-authored-by: Paul Jonas Jost <[email protected]> --------- Co-authored-by: Paul Jonas Jost <[email protected]>
* Hide result tab for multiple visualizations in case only one comparison was used. * Single tab is now selected, when multi comparisons are done, ocerall visualization is selected
* Fixed ID issue in cicerone. Fixed Markdown rendering instead of HTML rendering. Closes #392 * Update program/shinyApp/R/C.R Co-authored-by: Lea Seep <[email protected]> --------- Co-authored-by: Lea Seep <[email protected]>
* corrected pre-processing link * Reworked preprocessing helpfile and documentation * Fixed links and reworked heatmap * Considerably shorten the sample correlation * Updated DESeq to explain model factors (taken from question help). Question help not touched as i think having the explanation twice is good * Fixed link in data input. Adresses #390 partially * Added info that 1. annotation is optional and 2. what it puts out * Added note taking to the interface details. Partially adresses #365 * Reworked Significance Analysis. Closes #365 if sample correlation is fine.
* add workbook * linkt to additional resources * fix so that it opens in new tab
* add check for numerical data * download option, info to user * change misc shinyOmics to cOmicsArt * weaken NO check for nas in entities anno * usage of VI data if test are passing * insert checks; display data amtrix fixed; typos rm * add original row/colnames to respective anno tables * replaces now spaces with '.'
LeaSeep
approved these changes
Dec 6, 2024
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I think it would be good to merge everything into main again. We could start thinking about versioning if we want to as well, in which case this PR needs a Changelog