Merge pull request #146 from LeaSeep/pca_worflow_integrated

Pca worflow integrated
ICB-DCM · Dec 11, 2023 · a044abb · a044abb
2 parents 75d889d + d98116c
commit a044abb
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Showing 64 changed files with 2,429 additions and 1,701 deletions.
diff --git a/program/shinyApp/R/SourceAll.R b/program/shinyApp/R/SourceAll.R
@@ -1,6 +1,5 @@
 source("R/fun_filterRNA.R",local = T)
 source("R/fun_LFC.R",local = T)
-source("R/fun_volcano.R",local = T)
 source("R/fun_popupModal.R",local = T)
 source("R/heatmap/fun_entitieSelection.R",local = T)
 source("R/fun_savePheatmap.R",local = T)
@@ -16,7 +15,7 @@ source("R/enrichment_analysis/translation.R", local = T)
 source("R/enrichment_analysis/server.R", local = T)
 source("R/heatmap/server.R",local = T)
 source("R/pca/server.R", local = T)
-source("R/volcano_plot/server.R", local = T)
+source("R/pca/util.R", local = T)
 source("R/single_gene_visualisation/server.R",local = T)
 source("R/sample_correlation/server.R", local = T)
 source("R/significance_analysis/server.R", local = T)

diff --git a/program/shinyApp/R/data_selection/ui.R b/program/shinyApp/R/data_selection/ui.R
@@ -24,7 +24,7 @@ data_selection_sidebar_panel <- sidebarPanel(
   ),
   div(
     class = "DataSelection",
-    h4("Row selection -  biochemical entities"),
+    h4("Row selection - biochemical entities") %>% helper(type = "markdown", content = "DataSelection_RowSelection"),
     uiOutput(outputId = "providedRowAnnotationTypes_ui"),
     uiOutput(outputId = "row_selection_ui"),
     uiOutput(outputId = "propensityChoiceUser_ui")
@@ -58,38 +58,38 @@ data_selection_main_panel <- mainPanel(
         actionButton(
           inputId = "Reset",
           label = "Reset"
-        ),
+        ) %>% helper(type = "markdown", content = "DataSelection_Reset"),
         NULL
       ),
       hr(style = "border-top: 2px solid #90DBF4;"),
       a(id = "toggleAdvanced",
         "Data Upload via file input",
         style = "background-color: #90DBF4; color: black; padding: 7px 10px; "
-        ),
+        ) %>% helper(type = "markdown", content = "DataSelection_DataUploadFileInput"),
         shinyjs::hidden(
           div(
         id = "advanced",
         splitLayout(
           style = "border: 1px solid silver:", cellWidths = c("50%", "50%"),
-          uiOutput(outputId = "data_matrix1_ui"),
-          uiOutput(outputId = "data_sample_anno1_ui")
+          uiOutput(outputId = "data_matrix1_ui") %>% helper(type = "markdown", content = "DataSelection_Matrix"),
+          uiOutput(outputId = "data_sample_anno1_ui") %>% helper(type = "markdown", content = "DataSelection_SampleAnno")
         ),
         splitLayout(
           style = "border: 1px solid silver:", cellWidths = c("50%", "50%"),
-          uiOutput(outputId = "data_row_anno1_ui"),
+          uiOutput(outputId = "data_row_anno1_ui") %>% helper(type = "markdown", content = "DataSelection_RowAnno"),
           uiOutput(
             outputId = "data_preDone_ui"
-          ) %>% helper(type = "markdown", content = "SummarizedExp_help")
+          ) %>% helper(type = "markdown", content = "DataSelection_SummarizedExp")
         )
         )
       ),
       hr(style = "border-top: 2px solid #90DBF4;"),
-      uiOutput(outputId = "metadataInput_ui"),
+      uiOutput(outputId = "metadataInput_ui") %>% helper(type = "markdown", content = "DataSelection_MetaData"),
       hr(style = "border-top: 2px solid #90DBF4;"),
       downloadButton(
         outputId = "SaveInputAsList",
         label = "Save file input to upload later"
-      ) %>% helper(type = "markdown", content = "compilation_help"),
+      ) %>% helper(type = "markdown", content = "DataSelection_compilation_help"),
       htmlOutput(outputId = "debug", container = pre),
       HTML(text = "<br>"),
       HTML(text = "<br>")),
@@ -99,7 +99,7 @@ data_selection_main_panel <- mainPanel(
         actionButton(
           inputId = "DoVisualDataInspection",
           label = "Upload data for visual inspection"
-        ),
+        ) %>% helper(type = "markdown", content = "DataSelection_UploadInspection"),
         splitLayout(
           style = "border: 1px solid silver:", cellWidths = c("70%", "30%"),
           DT::dataTableOutput("DataMatrix_VI"),