release 0.1.3 #89

PaulJonasJost · 2022-12-02T09:35:04Z

General
- Fix various bugs (Fix 3 matrices data input Upload bug #78, Fix gather again #76, Fix overwriting of choices #84, Convience fixes #80, Fixes bug in snippet_dataInput #85, Fix scenario assignment and code creation #86, Catch a problem if there a no significant values. #91)
Significance Panel (Significance panel #81)
- allows for significance analysis of two conditions, multiple times
- choice of test, adjustment
- summary of each significance testing
- visualisations of summaries via VennDiagramm and UpSetR

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

LeaSeep

minor style things

LeaSeep · 2023-01-19T10:37:33Z

program/shinyApp/R/fun_getCurrentVersionFromChangeLog.R

@@ -0,0 +1,15 @@
+# Write function to insert current release absed on CHANGE log to DESCRIPTIOn
+# Return current version
+getCurrentVersion <- function(updateDESCRIPTION = T){


I know I have written this function but this variable is nowhere used...

LeaSeep · 2023-01-19T10:38:01Z

program/shinyApp/R/fun_ggplot.R

  if(numberOfScenario == 0){
-    stringtosave='# No_code_yet'
+    stringtosave <-'# No_code_yet'


Suggested change

stringtosave <-'# No_code_yet'

stringtosave <- '# No_code_yet'

LeaSeep · 2023-01-19T10:40:14Z

program/shinyApp/R/significance_analysis/server.R

+      # Print to report
+      observeEvent(input$only2Report_Sig,{
+        notificationID <- showNotification(ui = "Saving...",duration = 0)
+        tmp_filename <- paste0(getwd(),"/www/", paste(id,Sys.time(),".png",sep="_"))


Suggested change

tmp_filename <- paste0(getwd(),"/www/", paste(id,Sys.time(),".png",sep="_"))

tmp_filename <- paste0(getwd(),"/www/", paste(id,Sys.time(),".png", sep = "_"))

LeaSeep · 2023-01-19T10:40:41Z

program/shinyApp/R/significance_analysis/ui.R

@@ -0,0 +1,102 @@
+significance_analysis_sidebar_ui<- function(ns){


Suggested change

significance_analysis_sidebar_ui<- function(ns){

significance_analysis_sidebar_ui <- function(ns){

* 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]>

* Moved some stuff * Turned Aesthetics into conditional panels * Working conditional Panels. ConditionalPanels can get ns as argument * Removed LFC showing * Updating UI and moved static ui away from server * simplification of the server logic * removed logFoldChange switch * restructured and reworked entitie heatmap. Small todos left * choosing "all" possible * Report, Plot and Code * adjusted Code * Add modal in case of too many rows to warn. Also add option of no coloring

* Dokumentation for pre_process.md * adjust pre_process.md

* Moved some stuff * Turned Aesthetics into conditional panels * Working conditional Panels. ConditionalPanels can get ns as argument * Removed LFC showing * Updating UI and moved static ui away from server * simplification of the server logic * removed logFoldChange switch * restructured and reworked entitie heatmap. Small todos left * choosing "all" possible * Report, Plot and Code * adjusted Code * Made the heatmap save button functional * Working OA for heatmap genes * removed browser and minor bugfixes * None as default for color options * Continuing ven with large amounts of rows is possible now. * save genes button renamed * Update program/shinyApp/R/heatmap/ui.R Co-authored-by: Lea Seep <[email protected]> --------- Co-authored-by: Lea Seep <[email protected]>

* Data selection Documentation

* added function to check if ensmbl obj in www * added RDS object * moved definion of the organism up

* adding another soritn metric * heavy improving of helpfile * merge develop to update GSEA doc (#279)

* data selection tab report clean up * pre-processing report overworked with snippet * add sample correlation snippet; cahnge correlation as dist in smaple corr * Sample correlation snippet;personal notes advancements * PCA report and publication snippets * ajdusting volcano theme + removing table (dupl to sig ana) + sig ana snippet * add heatmap publication snippet * single gene fix anova mistake; publication snippet * logging brush up enrichment * add enrichment publication snippet; sort loggin new * make table chick * fix correlation method; added info to sig ana * add theme_bw

…ing. Copied line 814 with latest parameters into the preprocessing step, overwriting previously existing data. (#276)

* updating PCA * Sample correlation UI updating * Sig Ana update * Every UI should now update correctly

* First try for waiter * Waiter in all tasks * separate waiter for volcano * added library (needs add to renv as well)

* updated the test data to the one we used in screen record * Changed testdata rds.

* fixes and closes #281 * more custome theme; esspecially for download * add ggplot2 to correct postion * add check function to C as otherwise not found

* update renv + gitignore * removing error of PCA

* Heatmap working now * Removing sessions from functions. Sig Ana snippet works * Volcano Plot working * EA code snippet works * Added statistical sorting as well * merge Lea local work into Paul PR (#293) * adjusted Preface for the looks * forgot comma * add correct CUSTOM_THEME * fix heatmap snippet * finalising snippets * fix small bugs * fix small bugs ORA snippet --------- Co-authored-by: Lea Seep <[email protected]>

PaulJonasJost and others added 12 commits November 23, 2022 09:49

Merge pull request #75 from LeaSeep/main

0ee0018

Merge main into develop

Fix gather again (#76)

d084fa2

* hot fix * load tidyr package for gather fucntion

Fix overwriting of choices

5ab0853

Update program/shinyApp/R/enrichment_analysis/server.R

6318c65

Co-authored-by: Lea Seep <[email protected]>

Fix overwriting choices in UI

1e9562b

Fix overwriting of choices

Revert "Fix overwriting of choices" (#83)

0cfee4e

Fix overwriting of choices (#84)

5e831bb

Fixes bug in snippet_dataInput (#85)

38b4bc3

Fix scenario assignment and code creation (#86)

87a4f94

* Changes to ea. * Correct scenario assignment in ea. Also correct handling of modal pop-up

PaulJonasJost changed the title ~~release 0.13~~ release 0.1.2 Dec 2, 2022

PaulJonasJost changed the title ~~release 0.1.2~~ release 0.1.3 Dec 2, 2022

PaulJonasJost and others added 3 commits December 2, 2022 13:10

Catch a problem if there a no significant values. (#91)

d1c56d0

Prepare release v013 (#90)

9438a00

* 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]>

PaulJonasJost self-assigned this Dec 21, 2022

Merge branch 'main' into develop

d23d9ec

# Conflicts: # program/shinyApp/ui.R

PaulJonasJost added the ready for review label Dec 21, 2022

LeaSeep approved these changes Jan 19, 2023

View reviewed changes

This was referenced Jan 23, 2023

Significance Analysis - Visualisation #101

Closed

Upload of test-data even if data suplied #102

Closed

LeaSeep and others added 7 commits January 25, 2023 09:21

init res and par tmp; FLAG_TEST_DATA_SELECTEDto reactiveVal

348f228

changing input structure to SumExp

25fb67b

par_temp and res_temp added

2128251

fixed reactive Value; objects to res_tmp

0802f54

adjusting data selection to res_tmp object

2fb37a1

added par temp, res_temp to heatmap as well

c167611

PaulJonasJost added 2 commits July 10, 2024 23:06

Documentation pre process (#257)

c555ded

* Dokumentation for pre_process.md * adjust pre_process.md

PaulJonasJost temporarily deployed to github-pages July 10, 2024 21:15 — with GitHub Actions Inactive

Dokumentation for heatmap.md (#259)

1558c47

PaulJonasJost temporarily deployed to github-pages July 10, 2024 21:17 — with GitHub Actions Inactive

PaulJonasJost and others added 2 commits July 17, 2024 11:19

Enrichment analysis Documentation (#268)

80a27c4

PaulJonasJost temporarily deployed to github-pages July 18, 2024 08:50 — with GitHub Actions Inactive

Documentation of Data Selection (#269)

251e568

* Data selection Documentation

PaulJonasJost temporarily deployed to github-pages July 18, 2024 09:30 — with GitHub Actions Inactive

LeaSeep added 5 commits July 18, 2024 13:33

finally add sva - closes #221 (#272)

796fc5b

Fix database for annotation (#267)

a9d6c0f

* added function to check if ensmbl obj in www * added RDS object * moved definion of the organism up

added more meaningful descriptions (#274)

de5a690

bug fix rds ->RDS (#275)

bbdcb09

Add statistic sorting gsea (#270)

8e5c24c

* adding another soritn metric * heavy improving of helpfile * merge develop to update GSEA doc (#279)

LeaSeep temporarily deployed to github-pages July 23, 2024 12:11 — with GitHub Actions Inactive

LeaSeep and others added 13 commits July 24, 2024 11:15

Fixed bug, where preprocessed data was used for subsequent preprocess…

c7281de

…ing. Copied line 814 with latest parameters into the preprocessing step, overwriting previously existing data. (#276)

UI properly updating (#266)

84265c9

* updating PCA * Sample correlation UI updating * Sig Ana update * Every UI should now update correctly

Adding a "Waitress" while computing stuff (#271)

ffa39aa

* First try for waiter * Waiter in all tasks * separate waiter for volcano * added library (needs add to renv as well)

Updated testdata (#286)

608968a

* updated the test data to the one we used in screen record * Changed testdata rds.

HotFix: Waiter already needed in SourceAll.R

dd3884a

update renv + gitignore (#287)

9d5c585

Viz fixes (#285)

a17308d

* fixes and closes #281 * more custome theme; esspecially for download * add ggplot2 to correct postion * add check function to C as otherwise not found

Update small (#289)

2ab2a2d

* update renv + gitignore * removing error of PCA

added pictures of waiter. Closes #288

d19e18f

Changed custom_theme to CUSTOM_THEME to match C.R (#290)

ef7b417

Test data downloadable again (#297)

b08a2ec

PaulJonasJost merged commit 45d6839 into main Aug 8, 2024

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

release 0.1.3 #89

release 0.1.3 #89

PaulJonasJost commented Dec 2, 2022 •

edited

Loading

LeaSeep left a comment

LeaSeep Jan 19, 2023

LeaSeep Jan 19, 2023

LeaSeep Jan 19, 2023

LeaSeep Jan 19, 2023

	stringtosave <-'# No_code_yet'
	stringtosave <- '# No_code_yet'

	tmp_filename <- paste0(getwd(),"/www/", paste(id,Sys.time(),".png",sep="_"))
	tmp_filename <- paste0(getwd(),"/www/", paste(id,Sys.time(),".png", sep = "_"))

		@@ -0,0 +1,102 @@
		significance_analysis_sidebar_ui<- function(ns){

	significance_analysis_sidebar_ui<- function(ns){
	significance_analysis_sidebar_ui <- function(ns){

release 0.1.3 #89

release 0.1.3 #89

Conversation

PaulJonasJost commented Dec 2, 2022 • edited Loading

LeaSeep left a comment

Choose a reason for hiding this comment

LeaSeep Jan 19, 2023

Choose a reason for hiding this comment

LeaSeep Jan 19, 2023

Choose a reason for hiding this comment

LeaSeep Jan 19, 2023

Choose a reason for hiding this comment

LeaSeep Jan 19, 2023

Choose a reason for hiding this comment

PaulJonasJost commented Dec 2, 2022 •

edited

Loading