Merge branch 'develop' into hide_main_panelOptions

# Conflicts:
#	program/shinyApp/server.R

.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>"),

program/shinyApp/R/help_tab/ui.R

@@ -0,0 +1,81 @@
+help_tab_sidebar_panel <- sidebarPanel(
+  id = "sidebar_help_tab",
+  h4("Sidebar"),
+  div(id="firstQ",p("Here you can select parameters which are important for your analysis.") %>% helper(type = "markdown", content = "helpTab_question")),
+  br(),
+  div(
+    id = "ImageSelectArea",
+    shinyWidgets::virtualSelectInput(
+  inputId = "ImageSelect",
+  label = "Select Image",
+  choices = c("nothing selected", "WelcomePage", "YouTube Tutorial"),
+  selected = "nothing selected"
+  )
+  ),
+  # Horizontal line
+  actionButton(
+     inputId = "get_help",
+     label = "GO!",
+     icon = icon('paper-plane'),
+     style = "color: #fffff; background-color: #90DBF4; border-color: #000000"
+   ),
+  div(
+    id = "horizontalLine",
+    hr(style = "border-top: 1px solid #858585;")
+    ),
+  div(
+    id = "options",
+    sliderInput("ImageWidth",
+                label="image width",
+                min = 50, 
+                max = 100, 
+                post  = " %", 
+                value = 100),
+    radioButtons(
+      inputId = "ImageHeight",
+      label = "image height",
+      choices = c("300px","400px", "500px"),
+      selected = "400px",
+    )
+  )
+  # Add some option that renders the 
+  )
+
+
+
+help_tab_main_panel <- mainPanel(
+  id = "mainPanel_help_tab",
+  h4("Main Panel",id = "Test"),
+  actionButton("start_tour", span(icon("hand-pointer"),"Tour around cOmicsArt"),style = "background-color: #00c6ff; color: white; padding: 10px 20px; border-radius: 10px; transition: transform 0.2s;"),
+  div(
+    id = "help_tab_info",
+    htmlOutput(outputId = "help_tab_info", container = pre),
+  ),
+  uiOutput(outputId = "WelcomePage_ui"),
+  # Line break for additional spacing
+  br(),
+  div(
+    # Action button
+    actionButton(
+      inputId = "NextPanel",
+      label = "Take me to the Analysis Start",
+      width = "100%",
+      icon = icon('rocket'),
+      style = "color: #050505; background-color: #70BF4F47; border-color: #000000"
+    )
+  )
+
+)
+
+
+help_tab_panel <- tabPanel(
+  title = "Welcome to comicsArt ",
+  id = "help_tab",
+  fluid = T,
+  h4("User Help"),
+  ################################################################################
+  # Data Selection
+  ################################################################################
+  help_tab_sidebar_panel,
+  help_tab_main_panel
+)

program/shinyApp/helpfiles/DataSelection_DataUploadFileInput.md

@@ -1,6 +1,7 @@
 ### Data Upload via File Input
 
 ***
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/required-data-input.html" target="_blank">here</a>.
 
 With `Data upload` you can upload your data to the server via explicit csv files.<br>
 The files must be in the following format:<br>

program/shinyApp/helpfiles/DataSelection_MetaData.md

@@ -1,6 +1,7 @@
 ### Data Upload via File Input + Meta Data Sheet
 
 ***
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/required-data-input.html#starting-with-a-single-table-and-a-metadatasheet-" target="_blank">here</a>.
 
 With `Data upload` you can upload your data to the server via explicit csv files.<br>
 The files must be in the following format:<br>

program/shinyApp/helpfiles/DataSelection_RowSelection.md

@@ -1,6 +1,7 @@
 ### Data Selection by Columns and Rows
 
 ***
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/selection.html#row-selection---biochemical-entities" target="_blank">here</a>.
 
 With `Row selection` you can choose the entities (e.g. genes) you want to include in the 
 analysis.

program/shinyApp/helpfiles/DataSelection_SummarizedExp.md

@@ -1,6 +1,7 @@
 ### Data Upload via Precompiled Data
 
 ***
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/required-data-input.html#starting-with-an-rds-object" target="_blank">here</a>.
 
 With this option, you can upload previously used data. This allows you to upload 
 everything at once. Additionally, you can upload results from previous analyses. It is 

program/shinyApp/helpfiles/DataSelection_UploadInspection.md

@@ -1,6 +1,7 @@
 ### Data Quality Check - Visual Inspection
 
 ***
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/selection.html#file-input-%EF%B8%8F" target="_blank">here</a>.
 
 Using the `Upload visual inspection` tab, you can see the uploaded data and perform a 
 data quality check.

program/shinyApp/helpfiles/EA_GeneSets.md

@@ -1,5 +1,7 @@
 ## Gene Sets for Enrichment Analysis
 
+***
+
 You can choose a variety of gene sets for enrichment analysis. Here you find a 
 description of the gene sets. The information was taken from the
 [MSigDB database](https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp), where you 

program/shinyApp/helpfiles/EA_Options.md

@@ -1,6 +1,8 @@
 ## Enrichment Analysis Options
 
 ---
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/enrichment-analysis.html" target="_blank">here</a>.
+
 In cOmicsArt you can do either a gene set enrichment analysis or an over-representation analysis. The options for both analyses are described below.
 For more details read here on
 [Gene Set Enrichment Analysis](https://www.pnas.org/doi/abs/10.1073/pnas.0506580102) 

program/shinyApp/helpfiles/Heatmap_Aesthetics.md

@@ -1,6 +1,8 @@
 ## Heatmap Aesthetics Options
 
 ---
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/heatmap.html#aesthetics-options" target="_blank">here</a>.
+
 **1. Choose Variable to Color the Samples After:**
 
 - **Description:**

program/shinyApp/helpfiles/Heatmap_FurtherOptions.md

@@ -1,6 +1,8 @@
 ## Log Fold Change (LFC) Ordering Options
 
 ***
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/heatmap.html#conditional-options-for-top-k" target="_blank">here</a>.
+
 **1. Choose Type for LFC-Based Ordering:**
 
 - **Description:**

program/shinyApp/helpfiles/Heatmap_Options.md

@@ -1,8 +1,8 @@
-
----
-
 ## Row Selection Options
 
+***
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/heatmap.html#side-panel-" target="_blank">here</a>.
+
 **1. Row Selection Options:**
 
 - **Description**

program/shinyApp/helpfiles/Heatmap_RowAnnoBased.md

@@ -1,6 +1,7 @@
 ## Additional Row Selection Options
 
 ---
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/heatmap.html#conditional-options-for-select-based-on-annotation" target="_blank">here</a>.
 
 These options only make sense if you selected `rowAnno_based` in the `Row Selection`. 
 They serve to filter the row entities which to include in the heatmap.

program/shinyApp/helpfiles/PCA_Choices.md

@@ -1,6 +1,7 @@
 ## Principal Component Analysis (PCA) Options
 
 ***
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/pca.html#side-panel-" target="_blank">here</a>.
 
 A principal component analysis (PCA) is a linear dimensionality reduction technique to 
 visualize clusters within your data. For a small introduction on PCAs, please refer to 

program/shinyApp/helpfiles/PreProcessing_DESeqMain.md

@@ -1,5 +1,8 @@
 ## DESeq Factor Choices
 
+***
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/pre-processing.html" target="_blank">here</a>.
+
 ### Understanding the Design Matrix in DESeq2
 
 The design matrix in DESeq2 is a fundamental component used to specify the experimental design of your RNA-seq dataset. It helps in determining the relationship between the observed counts and the experimental conditions. Here's a detailed explanation:

program/shinyApp/helpfiles/PreProcessing_Procedures.md

@@ -1,4 +1,6 @@
 ## Data Preprocessing
+***
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/pre-processing.html" target="_blank">here</a>.
 
 **Step 1: General Data Cleaning**
 

program/shinyApp/helpfiles/SampleCorr_Choices.md

@@ -1,6 +1,7 @@
 ## Correlation method
 
 ***
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/sample-correlation.html" target="_blank">here</a>.
 
 Choose **one** of the following correlation methods. These correlation methods provide 
 insights into different aspects of relationships between variables. Understanding 

program/shinyApp/helpfiles/SampleCorr_Color.md

@@ -1,6 +1,7 @@
 ## Color Annotation
 
 ***
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/sample-correlation.html" target="_blank">here</a>.
 
 You can choose **Multiple** options. Each option is a column from the `sample 
 annotation table`. The clustered samples will be colored on the right side by your 

program/shinyApp/helpfiles/SampleCorr_Downloads.md

@@ -1,6 +1,7 @@
 ## Download Helper
 
 ***
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details.html#features-across-tabs" target="_blank">here</a>.
 
 These buttons serve for various downloading purposes.
 

program/shinyApp/helpfiles/SigAna_Choices.md

@@ -1,5 +1,8 @@
 ## Significance Analysis Options
 
+***
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/significance-analysis.html#main-panel-" target="_blank">here</a>.
+
 **1. Choose Groups to Compare:**
 
 - **Description:**

program/shinyApp/helpfiles/SigAna_Intersections.md

@@ -1,6 +1,8 @@
 ## Highlight and Download intersections
 
 ***
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/significance-analysis.html#main-panel-" target="_blank">here</a>.
+
 To allow for a better overview of the intersections, the user can highlight the 
 intersections of interest. You can choose from all available intersections in the 
 `Intersections to highlight` menu. The intersection names shown in the Upset plot above, 

program/shinyApp/helpfiles/SigAna_Vis.md

@@ -1,6 +1,8 @@
 ## Visualizing Significance Analysis Results Options
 
 ***
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/significance-analysis.html#main-panel-" target="_blank">here</a>.
+
 **1. Select Comparisons to Visualize:**
 
 - **Description:**

program/shinyApp/helpfiles/SingleGene_Options.md

@@ -1,6 +1,8 @@
 ## Single Gene Visualization Options
 
 ---
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/single-gene-visualisations.html#side-panel-" target="_blank">here</a>.
+
 **1. Choose Data Type:**
 
 - **Description:**

program/shinyApp/helpfiles/SingleGene_Select.md

@@ -1,6 +1,8 @@
 ## Choosing groups for comparison
 
 ---
+💡 **Tip**: For more detailed information, please visit <a href="https://icb-dcm.github.io/cOmicsArt/interface-details/single-gene-visualisations.html#side-panel-" target="_blank">here</a>.
+
 This option lets you specify how to group the samples based on the annotation categories 
 provided in the sample annotation file. This only has an effect if you have chosen 
 `boxplots_withTesting` as the visualization style.