Merge branch 'develop' into DESeq2_removal

.github/workflows/start_check.yaml

@@ -103,6 +103,7 @@ jobs:
         if (result == "Success") {
           cat("Test passed")
         } else {
+        cat(result)
            cat("Test failed: Output is 'failure'\n")
           quit(status = 1)
         }

docs/index.md

@@ -12,7 +12,7 @@ nav_exclude: true
 
 If you are looking for the web app, please visit: 🌐 [cOmicsART Web App](https://shiny.iaas.uni-bonn.de/cOmicsArt/)
 
-Otherwise, you can navigate through the documentation using the sidebar on the left. If you’re searching for something specific, try using the search bar at the top. 🔍 It can search through the entire documentation and guide you to the relevant section.
+Otherwise, you can navigate through the documentation using the sidebar on the left. **If you’re searching for something specific, try using the search bar at the top.** 🔍 It can search through the entire documentation and guide you to the relevant section.
 
 Have fun exploring! 🎉
 

docs/welcome.md

@@ -11,7 +11,7 @@ nav_order: 1
 
 If you are looking for the web app, please visit: 🌐 [cOmicsART Web App](https://shiny.iaas.uni-bonn.de/cOmicsArt/)
 
-Otherwise, you can navigate through the documentation using the sidebar on the left. If you’re searching for something specific, try using the search bar at the top. 🔍 It can search through the entire documentation and guide you to the relevant section.
+Otherwise, you can navigate through the documentation using the sidebar on the left. **If you’re searching for something specific, try using the search bar at the top.** 🔍 It can search through the entire documentation and guide you to the relevant section.
 
 **Have fun exploring!** 🎉
 

program/shinyApp/R/C.R

@@ -1,6 +1,7 @@
 # Keep here for now. Needs to be replaced i guess at some point.
 library(waiter)
 library(ggplot2)
+library(cicerone)
 ### Global Constants will be saved here
 NOTES_PlACEHOLDER <<- "Notes you want to take alongside the plot (will be saved in the report) \nYou can use markdown syntax for your notes "
 NOTES_HELP <<- HTML("<a href='https://www.markdownguide.org/cheat-sheet/' target='_blank'>Here you can find a Markdown Cheat Sheet</a> \n
@@ -237,4 +238,82 @@ LOADING_SCREEN <- tagList(
       )
     )
   )
-)
+)
+
+
+
+guide <<- cicerone::Cicerone$
+  new(keyboard_control = TRUE)$
+  step(
+    el = "sidebar_help_tab",
+    title = "This is the Sidebar",
+    position = "right",
+    description = HTML("Always start here to give cOmicsArt tasks.<br>We will go through the elements step by step."),
+  )$
+  step(
+    el = "ImageSelectArea",
+    position = "right",
+    title = "Important parameters for the analysis",
+    description = HTML("Here we have 1 parameter to set.<br> Select 'Youtube Tutorial' from the dropdown menu.")
+  )$
+  step(
+    el = "horizontalLine",
+    title = "An important line",
+    description = HTML("All options above this line require re-computation, which is done by pressing the 'GO!' button. <br>All options below this line can be always changed.")
+  )$
+  step(
+    el = "get_help",
+    title = "The Go button evokes (re-)computation",
+    description = "Press it now to continue."
+  )$
+  step(
+    el = "mainPanel_help_tab",
+    title = "This is the main panel",
+    description = HTML("Here your output is displayed.<br>We will go through the elements step by step in a second.")
+  )$
+  step(
+    el = "help_tab_info",
+    title = "Information box",
+    description = HTML("Contains information about the performed analysis.<br> For example: It will notify you if the analysis was successful or if there were any warning.<br> **It is always a good idea to pay attention to the output here.**")
+  )$
+  step(
+    el ="mainPanel_help_tab",
+    title = "Display of computed results",
+    position = "mid-center",
+    description = HTML("If you have selected Youtube Tutorial AND pressed the 'GO' button you will see a video here. <br>You might want to watch it after this little guide to get introduced to the analysis features).")
+  )$
+  step(
+    el = "options",
+    title = "Here you can play around",
+    description = "Here, we have the options the adjust the width and height of the image.<br>A change will be reflected in the output immediately."
+  )$
+  step(
+    el = "NextPanel",
+    title = "Next Panel",
+    description = "This button will take you to the next panel to start."
+  )$
+  step(
+    el = "tabsetPanel1",
+    title = "currently available Analysis Tabs",
+    description = HTML("You can switch between them by clicking on the tab names.<br>Note, that more tabs will appear after the mandatory tabs:<br>1. Data selection <br>2. Pre-processing (not visible yet).<br>
+    As soon as the Pre-processing is done the analysis tabs will appear. They work independently from each other.")
+  )$
+  step(
+    el = "firstQ",
+    title = "Question Marks lead to help",
+    description = "Useful to get more help on the particular tagged item."
+  )$
+  step(
+    el = "UsefulLinks",
+    title = "Very Useful Links",
+description = HTML("The top one let's you get the automatic generated report.<br> The bottom leads you to the *extensive* Documentation. Click it now!")
+  )$
+  step(
+    el = "WelcomePage_ui",
+    title = "The End",
+    description = "
+    <p>This is the end of the little tutorial. If you'd like more specific help about cOmicsArt in action, check out the <a href='https://www.youtube.com/watch?v=pTGjtIYQOak&t=2s' target='_blank'>YouTube Tutorial</a>!</p>
+    <p>You can also visit the <a href='https://icb-dcm.github.io/cOmicsArt/' target='_blank'>documentation</a> for more detailed information.</p>
+    <p>After this tutorial, you should be able to find the link within the interface on your own. Happy exploring! <i class='fas fa-cat'></i> </p>
+  "
+    )

program/shinyApp/R/data_selection/ui.R

@@ -89,7 +89,7 @@ data_selection_sidebar_panel <- sidebarPanel(
           label = HTML('Upload data matrix <br/><small>(rows entities, cols samples) <br/><a href="airway-read-counts-LS.csv" download>Download example data (Transcriptomics, human)</a></small>'),
           accept = c(".csv", ".xlsx"),
           width = "80%"
-        ) %>% helper(type = "markdown", content = "DataSelection_MetaData"),
+        ) %>% helper(type = "markdown", content = "DataSelection_MetaData",style = "font-size: 24px;"),
         shiny::fileInput(
           inputId = "metadataInput",
           label = HTML("Upload your Meta Data Sheet <small>(currently replaces sample annotation)</small>"),
@@ -139,12 +139,24 @@ data_selection_sidebar_panel <- sidebarPanel(
 
 data_selection_main_panel <- mainPanel(
   id = "mainPanel_DataSelection",
-  div(
+  div(id ="InfoBox_DataSelection",
+      htmlOutput(outputId = "debug", container = pre)
+      ),
+  # add link to toggle on the div geneAnno_toggle
+  actionButton(
+    inputId = "geneAnno_toggle_button",
+    label = "(show/hide) Further entitie Annotation options",
+    icon = icon('plus'),
+    style = "color: #000000; background-color: transparent; border-color: transparent"
+  ),
+  div( 
+    id  = "geneAnno_toggle",
+    style = "display: none;",
     class = "AddGeneSymbols_ui",
     uiOutput("AddGeneSymbols_organism_ui"),
-    uiOutput("AddGeneSymbols_ui")
+    uiOutput("AddGeneSymbols_ui"),
+    hr(style = "border-top: 1px solid #858585;")
   ),
-  hr(style = "border-top: 1px solid #858585;"),
   fluidRow(
     column(5,
            div(class = "DataSelection",
@@ -160,15 +172,13 @@ data_selection_main_panel <- mainPanel(
                uiOutput("sample_selection_ui")
            ))
   ),
-  hr(style = "border-top: 1px solid #858585;"),
   div(
     id = "SaveInputAsRDS",
     downloadButton(
       outputId = "SaveInputAsList",
       label = "Save file input to upload later"
     ) %>% helper(type = "markdown", content = "DataSelection_compilation_help")
   ),
-  htmlOutput(outputId = "debug", container = pre),
   br(), br(), br(),
   hr(style = "border-top: 1px solid #858585;"),
   actionButton(

program/shinyApp/R/enrichment_analysis/server.R

@@ -19,23 +19,28 @@ enrichment_analysis_geneset_server <- function(
         print(result)
         # Enrichment Result Plot
         # only plot if the best found adjustment value is significant
-        if(result@result$p.adjust[1] < 0.05){
-          showElement(id = "EnrichmentPlot")
-          showElement(id = "only2Report")
-          showElement(id = "getR_Code")
-          showElement(id = "SavePlot")
-          showElement(id = "file_ext")
-          showElement(id = "Notes")
-          showElement(id = "NotesHelper")
-          hideElement(id = "EnrichmentFailure")
-          output$EnrichmentPlot <- renderPlot({clusterProfiler::dotplot(result) + CUSTOM_THEME})
-          if(ea_type == "GeneSetEnrichment"){
-            ea_scenario <- 15
-          }else{
-            ea_scenario <- 14
+        if(nrow(result@result) > 0){
+          if(result@result$p.adjust[1] < 0.05){
+            showElement(id = "EnrichmentPlot")
+            showElement(id = "only2Report")
+            showElement(id = "getR_Code")
+            showElement(id = "SavePlot")
+            showElement(id = "file_ext")
+            showElement(id = "Notes")
+            showElement(id = "NotesHelper")
+            hideElement(id = "EnrichmentFailure")
+            output$EnrichmentPlot <- renderPlot({clusterProfiler::dotplot(result) + CUSTOM_THEME})
+            if(ea_type == "GeneSetEnrichment"){
+              ea_scenario <- 15
+            }else{
+              ea_scenario <- 14
+            }
+          }else{ # print that no significant result was found
+            showElement(id = "EnrichmentFailure")
+            output$EnrichmentFailure <- renderText("No significant result found. For further details check the table.")
+            ea_scenario <- 0
           }
-        }
-        else{ # print that no significant result was found
+        }else{ # print that no significant result was found
           showElement(id = "EnrichmentFailure")
           output$EnrichmentFailure <- renderText("No significant result found. For further details check the table.")
           ea_scenario <- 0
@@ -209,6 +214,7 @@ enrichment_analysis_Server <- function(id, data, params, updates){
         organism = NULL
       )
       ns <- session$ns
+      output$EnrichmentInfo <- renderText({"Press 'Get Enrichment Analysis' to start. Note that this analysis is only meaningful for gene sets at the moment."})
       ## initialize result as NULL
       ea_reactives$enrichment_results <- ENRICHMENT_RESULT_RESET
       # TODO: Call this in a loop.
@@ -494,6 +500,7 @@ enrichment_analysis_Server <- function(id, data, params, updates){
         geneSetChoice_tmp
       })
       observeEvent(input$enrichmentGO,{
+        shinyjs::showElement(id = "enrichment_div", asis = TRUE)
         ea_reactives$ea_info <- "Enrichment is running..."
         waiter <- Waiter$new(
           html = LOADING_SCREEN,

program/shinyApp/R/enrichment_analysis/ui.R

@@ -120,65 +120,67 @@ ea_sidebar <- function(ns){
 ea_main <- function(ns){
   mainPanel(
     textOutput(outputId = ns("EnrichmentInfo"), container = pre),
-    tabsetPanel(
-      id = ns("EnrichmentTabs"),
-      geneset_panel_UI(ns("Hallmarks")),
-      geneset_panel_UI(ns("C1")),
-      geneset_panel_UI(ns("C2")),
-      geneset_panel_UI(ns("CGP")),
-      geneset_panel_UI(ns("CP")),
-      geneset_panel_UI(ns("BIOCARTA")),
-      geneset_panel_UI(ns("KEGG")),
-      geneset_panel_UI(ns("PID")),
-      geneset_panel_UI(ns("REACTOME")),
-      geneset_panel_UI(ns("WIKIPATHWAYS")),
-      geneset_panel_UI(ns("C3")),
-      geneset_panel_UI(ns("MIRDB")),
-      geneset_panel_UI(ns("MIR_Legacy")),
-      geneset_panel_UI(ns("GTRD")),
-      geneset_panel_UI(ns("TFT_Legacy")),
-      geneset_panel_UI(ns("C4")),
-      geneset_panel_UI(ns("CGN")),
-      geneset_panel_UI(ns("CM")),
-      geneset_panel_UI(ns("C5")),
-      geneset_panel_UI(ns("GO")),
-      geneset_panel_UI(ns("GO_BP")),
-      geneset_panel_UI(ns("GO_CC")),
-      geneset_panel_UI(ns("GO_MF")),
-      geneset_panel_UI(ns("HPO")),
-      geneset_panel_UI(ns("C6")),
-      geneset_panel_UI(ns("C7")),
-      geneset_panel_UI(ns("IMMUNESIGDB")),
-      geneset_panel_UI(ns("VAX")),
-      geneset_panel_UI(ns("C8")),
-      tabPanel(
-        title = "KeggPathwayOutput",
-        helpText("Specificy on the left which pathway (all sig. enriched) to display in picture-format"),
-        actionButton(
-          inputId = ns("OverlayOnPathway"),
-          label = "Show overlay on Pathway"
-        ),
-        selectInput(
-          inputId = ns("plotOnTopOption"),
-          label = "Specifiy the what the colored overlay should indicate",
-          choices = c("LFC", "presence"),
-          selected = "presence"
-        ),
-        uiOutput(outputId = ns("sample_anno_types_KEGG_ui")),
-        uiOutput(outputId = ns("ComparisonOptionsCRTL_ui")),
-        uiOutput(outputId = ns("ComparisonOptionsCOMP_ui")),
-        uiOutput(outputId = ns("psig_KEGG_ui")),
-        sliderInput(
-          inputId = ns("imageWidth"),
-          label = "Adjust Width",
-          min = 400, max = 1500, step = 20, value = 1000
-        ),
-        sliderInput(
-          inputId = ns("imageHeight"),
-          label = "Adjust Height",
-          min = 400, max = 1500, step = 20, value = 640
-        ),
-        imageOutput(outputId = ns("KeggPathwayOutput_img"))
+    div(id = "enrichment_div",
+      tabsetPanel(
+        id = ns("EnrichmentTabs"),
+        geneset_panel_UI(ns("Hallmarks")),
+        geneset_panel_UI(ns("C1")),
+        geneset_panel_UI(ns("C2")),
+        geneset_panel_UI(ns("CGP")),
+        geneset_panel_UI(ns("CP")),
+        geneset_panel_UI(ns("BIOCARTA")),
+        geneset_panel_UI(ns("KEGG")),
+        geneset_panel_UI(ns("PID")),
+        geneset_panel_UI(ns("REACTOME")),
+        geneset_panel_UI(ns("WIKIPATHWAYS")),
+        geneset_panel_UI(ns("C3")),
+        geneset_panel_UI(ns("MIRDB")),
+        geneset_panel_UI(ns("MIR_Legacy")),
+        geneset_panel_UI(ns("GTRD")),
+        geneset_panel_UI(ns("TFT_Legacy")),
+        geneset_panel_UI(ns("C4")),
+        geneset_panel_UI(ns("CGN")),
+        geneset_panel_UI(ns("CM")),
+        geneset_panel_UI(ns("C5")),
+        geneset_panel_UI(ns("GO")),
+        geneset_panel_UI(ns("GO_BP")),
+        geneset_panel_UI(ns("GO_CC")),
+        geneset_panel_UI(ns("GO_MF")),
+        geneset_panel_UI(ns("HPO")),
+        geneset_panel_UI(ns("C6")),
+        geneset_panel_UI(ns("C7")),
+        geneset_panel_UI(ns("IMMUNESIGDB")),
+        geneset_panel_UI(ns("VAX")),
+        geneset_panel_UI(ns("C8")),
+        tabPanel(
+          title = "KeggPathwayOutput",
+          helpText("Specificy on the left which pathway (all sig. enriched) to display in picture-format"),
+          actionButton(
+            inputId = ns("OverlayOnPathway"),
+            label = "Show overlay on Pathway"
+          ),
+          selectInput(
+            inputId = ns("plotOnTopOption"),
+            label = "Specifiy the what the colored overlay should indicate",
+            choices = c("LFC", "presence"),
+            selected = "presence"
+          ),
+          uiOutput(outputId = ns("sample_anno_types_KEGG_ui")),
+          uiOutput(outputId = ns("ComparisonOptionsCRTL_ui")),
+          uiOutput(outputId = ns("ComparisonOptionsCOMP_ui")),
+          uiOutput(outputId = ns("psig_KEGG_ui")),
+          sliderInput(
+            inputId = ns("imageWidth"),
+            label = "Adjust Width",
+            min = 400, max = 1500, step = 20, value = 1000
+          ),
+          sliderInput(
+            inputId = ns("imageHeight"),
+            label = "Adjust Height",
+            min = 400, max = 1500, step = 20, value = 640
+          ),
+          imageOutput(outputId = ns("KeggPathwayOutput_img"))
+        )
       )
     )
   )
@@ -194,7 +196,6 @@ enrichment_analysis_UI <- function(id){
     #########################################
     # Enrichment
     #########################################
-    h4("NOTE THAT THIS ONLY MAKES SENSE FOR TRANSCRIPTOMICS DATA AT THE MOMENT!"),
     ea_sidebar(ns),
     ea_main(ns),
   )