Merge pull request #43 from LeaSeep/develop

release 0.1.0
ICB-DCM · Nov 10, 2022 · dd20571 · dd20571
2 parents 2a18eea + 6b5817c
commit dd20571
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,21 @@
+Release notes
+=============
+
+
+0.1 series
+..........
+
+
+0.1.0 (2022-10-25)
+-------------------
+* General:
+  * Renamed `Project to lower Dimension` to `PCA` (#10)
+  * Modularization (#11, #13, #24, #25, #27, #28, #26, #38)
+  * bug fixes(#14, #16, #33, #34, #36, #39)
+  * Coding Style (#20, #21)
+  * Added changelog (#49)
+* Sample Correlation:
+  * New Module (#35)
+* Enrichment Analysis:
+  * Additional Gene set allowed + selection (#41 , #22 )
+  * fixed ORA (#48)
diff --git a/program/renv.lock b/program/renv.lock
@@ -672,6 +672,17 @@
       "Hash": "50c838a310445e954bc13f26f26a6ecf",
       "Requirements": []
     },
+    "babelgene": {
+      "Package": "babelgene",
+      "Version": "22.9",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "8288e81d0c2c3272603f6ef394ffa6fd",
+      "Requirements": [
+        "dplyr",
+        "rlang"
+      ]
+    },
     "backports": {
       "Package": "backports",
       "Version": "1.4.1",
@@ -1845,6 +1856,21 @@
         "Rcpp"
       ]
     },
+    "msigdbr": {
+      "Package": "msigdbr",
+      "Version": "7.5.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "2def1d52dfe1044f82e75d25fb5dd2e5",
+      "Requirements": [
+        "babelgene",
+        "dplyr",
+        "magrittr",
+        "rlang",
+        "tibble",
+        "tidyselect"
+      ]
+    },
     "munsell": {
       "Package": "munsell",
       "Version": "0.5.0",

diff --git a/program/shinyApp/R/C.R b/program/shinyApp/R/C.R
@@ -0,0 +1,20 @@
+### Global Constants will be saved here
+
+NOTES_PlACEHOLDER <- "Notes you want to take alongside the Plot (will be saved in the report) \nYou may want to use markdown syntay for structering the notes "
+NOTES_HELP <- "Notes: For structure reasons you should start with Heading Level 4 (hence #### My personal Title)"
+
+CODE_DOWNLOAD_PREFACE <- "# ShinyOmics R Code Download\n# Load necassary packages (if errors please install respective packages)
+library(ggplot2)
+library(ggpubr)
+library(rstudioapi)
+# if not run in RStudio  you need to specify the directory fo the file yourself!
+
+direcoty_of_files=dirname(rstudioapi::getSourceEditorContext()$path)
+envList=readRDS(paste0(direcoty_of_files,'/','Data.rds'))  
+
+list2env(envList,envir = globalenv()) 
+# loads the varaibles directly into global env
+# if you want to combine multiple plots use the `with` notation instead e.g.
+# plot <- with(envList, {ggplot(..)+geom_point()})
+  
+# Happy Adjusting! :)"
diff --git a/program/shinyApp/R/data_selection/ui.R b/program/shinyApp/R/data_selection/ui.R
@@ -0,0 +1,117 @@
+data_selection_sidebar_panel <- sidebarPanel(
+  id = "sidebar_data_selection",
+  div(class = "omicType",
+      selectInput(
+        inputId = "omicType", # RNAorLIPID
+        label = "Omic Type that is uploaded",
+        choices = c("Transcriptomics", "Lipidomics", "Metabolomics"),
+        selected = ""
+      )
+  ),
+  div(
+    class = "AddGeneSymbols_ui",
+    uiOutput(outputId = "AddGeneSymbols_ui"),
+    uiOutput(outputId = "AddGeneSymbols_organism_ui")
+  ),
+  #uiOutput("AddGeneSymbols_organism_ui"),
+  actionButton(
+    inputId = "refresh1",
+    label = "Do"
+  ),
+  div(
+    class = "LineToDistinguish",
+    hr(style = "border-top: 1px solid #000000;")
+  ),
+  div(
+    class = "DataSelection",
+    h4("Row selection -  biochemical entities"),
+    uiOutput(outputId = "providedRowAnnotationTypes_ui"),
+    uiOutput(outputId = "row_selection_ui"),
+    uiOutput(outputId = "propensityChoiceUser_ui")
+  ),
+  # Outlier Selection -> for fixed removal pre-processing needs to be redone!
+  div(
+    class = "SampleSelection",
+    h4("Sample selection"),
+    uiOutput(outputId = "providedSampleAnnotationTypes_ui"),
+    uiOutput(outputId = "sample_selection_ui")),
+    uiOutput(outputId = "NextPanel_ui")
+)
+
+
+data_selection_main_panel <- mainPanel(
+  id = "mainPanel_DataSelection",
+  tabsetPanel(
+    type = "pills",
+    tabPanel(
+      title = "Upload section",
+      splitLayout(
+        style = "border: 1px solid silver:", cellWidths = c("85%", "10%", "5%"),
+        NULL,
+        actionButton(
+          inputId = "Reset",
+          label = "Reset"
+        ),
+        NULL
+      ),
+      splitLayout(
+        style = "border: 1px solid silver:", cellWidths = c("50%", "50%"),
+        uiOutput(outputId = "data_matrix1_ui"),
+        uiOutput(outputId = "data_sample_anno1_ui")
+      ),
+      splitLayout(
+        style = "border: 1px solid silver:", cellWidths = c("50%", "50%"),
+        uiOutput(outputId = "data_row_anno1_ui"),
+        uiOutput(
+          outputId = "data_preDone_ui"
+        ) %>% helper(type = "markdown", content = "SummarizedExp_help")
+      ),
+      hr(style = "border-top: 2px solid #cbedca;"),
+      uiOutput(outputId = "metadataInput_ui"),
+      hr(style = "border-top: 2px solid #cbedca;"),
+      downloadButton(
+        outputId = "SaveInputAsList",
+        label = "Save file input to upload later"
+      ) %>% helper(type = "markdown", content = "compilation_help"),
+      htmlOutput(outputId = "debug", container = pre),
+      HTML(text = "<br>"),
+      HTML(text = "<br>")),
+      tabPanel(
+        title = "Upload visual inspection",
+        helpText("If you have uploaded your data, you might want to visually check the tables to confirm the correct data format. If you notice irregualarities you will need to correct the input data - this cannot be done in ShinyOmics, See the help on how your data is expected."),
+        actionButton(
+          inputId = "DoVisualDataInspection",
+          label = "Upload data for visual inspection"
+        ),
+        splitLayout(
+          style = "border: 1px solid silver:", cellWidths = c("70%", "30%"),
+          DT::dataTableOutput("DataMatrix_VI"),
+          htmlOutput(outputId = "DataMatrix_VI_Info", container = pre)
+        ),
+        splitLayout(
+          style = "border: 1px solid silver:", cellWidths = c("70%", "30%"),
+          DT::dataTableOutput("SampleMatrix_VI"),
+          htmlOutput(outputId = "SampleMatrix_VI_Info", container = pre)
+        ),
+        splitLayout(
+          style = "border: 1px solid silver:", cellWidths = c("70%", "30%"),
+          DT::dataTableOutput("EntitieMatrix_VI"),
+          htmlOutput(outputId = "EntitieMatrix_VI_Info", container = pre)
+        ),
+        htmlOutput(outputId = "OverallChecks", container = pre)
+      )
+  )
+)
+
+
+data_selection_panel <- tabPanel(
+  title = "Data selection",
+  id = "Data_selection",
+  fluid = T,
+  h4("Data Selection"),
+  ################################################################################
+  # Data Selection
+  ################################################################################
+  data_selection_sidebar_panel,
+  data_selection_main_panel
+)
diff --git a/program/shinyApp/R/enrichment_analysis/check_annotation.R b/program/shinyApp/R/enrichment_analysis/check_annotation.R
@@ -0,0 +1,39 @@
+check_annotation_enrichment_analysis <- function(){
+  # allowed annotations
+  ensembl_opt <- c(
+    "ensembl", "Ensembl", "ensembl_id", "Ensembl_ID", "Ensemble ID", "ENSEMBL"
+  )
+  entrez_opt <- c(
+    "entrez", "Entrez", "entrez_id", "Entrez_ID", "Entrez ID", "Entrez Gene ID", "ENTREZID"
+  )
+  symbol_opt <- c(
+    "symbol", "Symbol", "gene_symbol", "Gene_Symbol", "Gene Symbol", "Nomenclature", "SYMBOL"
+  )
+  # check if annotation is in row-annotation
+  no_ann <- TRUE  # TRUE if no annotation is found
+  entrez_ann <- FALSE  # TRUE if no entrez annotation is found
+  base_annotation <- NULL  # annotation to be used in translation
+  if (any(entrez_opt %in% colnames(processedData_all$Transcriptomics$annotation_rows))){
+    names(processedData_all$Transcriptomics$annotation_rows)[names(processedData_all$Transcriptomics$annotation_rows) == entrez_opt[entrez_opt %in% colnames(processedData_all$Transcriptomics$annotation_rows)]] <<- "ENTREZID"
+    no_ann <- FALSE
+    entrez_ann <- FALSE
+    base_annotation <- "ENTREZID"
+  }
+  if (any(ensembl_opt %in% colnames(processedData_all$Transcriptomics$annotation_rows))){
+    names(processedData_all$Transcriptomics$annotation_rows)[names(processedData_all$Transcriptomics$annotation_rows) == ensembl_opt[ensembl_opt %in% colnames(processedData_all$Transcriptomics$annotation_rows)]] <<- "ENSEMBL"
+    no_ann <- FALSE
+    base_annotation <- "ENSEMBL"
+  }
+  if (any(symbol_opt %in% colnames(processedData_all$Transcriptomics$annotation_rows))){
+    names(processedData_all$Transcriptomics$annotation_rows)[names(processedData_all$Transcriptomics$annotation_rows) == symbol_opt[symbol_opt %in% colnames(processedData_all$Transcriptomics$annotation_rows)]] <<- "SYMBOL"
+    no_ann <- FALSE
+    base_annotation <- "SYMBOL"
+  }
+  no_ann <- TRUE
+  # if no annotation is found, add popup asking for annotation
+  return(list(
+    "no_ann" = no_ann,
+    "entrezid_ann" = entrez_ann,
+    "base_annotation" = base_annotation
+  ))
+}