Fix 3 matrices data input Upload bug (#78)

* 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 <70631928+PaulJonasJost@users.noreply.github.com>

program/shinyApp/R/pca/server.R

@@ -526,7 +526,7 @@ pca_Server <- function(id, omic_type, row_select){
         entitiesToInclude <- apply(df_loadings_filtered, 1, any)
 
         df_loadings <- df_loadings[entitiesToInclude,] %>%
-          gather(key = "PC", value = "loading", -entity)
+          tidyr::gather(key = "PC", value = "loading", -entity)
 
         global_max <- max(df_loadings$loading)
         global_min <- -global_max

program/shinyApp/server.R

@@ -230,8 +230,14 @@ server <- function(input,output,session){
        file = input$data_matrix1$datapath,
        header = T,
        row.names = 1,
-       check.names = F
+       check.names = T
        )
+     Matrix2 <- read.csv(
+       file = input$data_matrix1$datapath,
+       header = T,
+       row.names = 1,
+       check.names = F
+     )
      output$DataMatrix_VI <- DT::renderDataTable({
        DT::datatable(data = Matrix)
        })
@@ -271,11 +277,12 @@ server <- function(input,output,session){
        "
        })
 
-     check1 <- ifelse(all(rownames(Matrix)==rownames(annotation_rows)),snippetYes,snippetNo)
-     check2 <- ifelse(all(colnames(Matrix)==rownames(sample_table)),snippetYes,snippetNo)
-     check3 <- ifelse(any(is.na(Matrix)==T),snippetNo,snippetYes)
-     check4 <- ifelse(any(is.na(sample_table)==T),snippetNo,snippetYes)
-     check5 <- ifelse(any(is.na(annotation_rows)==T),snippetNo,snippetYes)
+     check1 <- ifelse(all(rownames(Matrix) == rownames(annotation_rows)),snippetYes,snippetNo)
+     check2 <- ifelse(all(colnames(Matrix) == rownames(sample_table)),snippetYes,snippetNo)
+     check3 <- ifelse(any(is.na(Matrix) == T),snippetNo,snippetYes)
+     check4 <- ifelse(any(is.na(sample_table) == T),snippetNo,snippetYes)
+     check5 <- ifelse(any(is.na(annotation_rows) == T),snippetNo,snippetYes)
+     check6 <- ifelse(all(colnames(Matrix2) == colnames(Matrix)),snippetYes,snippetNo)
 
      if(check5 == snippetNo){
        # Indicate columns with NA
@@ -288,13 +295,23 @@ server <- function(input,output,session){
        check5 <- paste0(snippetNo," Following columns are potentially problematic: ",paste0(colsWithNa, collapse = ", "))
      }
 
+     if(check6 == snippetNo){
+       # add help text
+       check6 <- paste0(
+         snippetNo,
+         "\n\t A syntactically valid name consists of letters, numbers and the dot or underline characters \n
+         and starts with a letter or the dot not followed by a number.\n
+         Therefore '12345' is invalid, 'ID_12345' is valid \n
+         Remember to change the Sample ID everywhere (Matrix & Sample Table")
+     }
      output$OverallChecks <- renderText({
        paste0("Some overall Checks are running run ...\n
        Rownames of Matrix are the same as rownames of entitie table ",check1,"\n
        Colnames of Matrix are same as rownames of sample table ",check2," \n
        Matrix has no na ",check3,"\n
        Sample table no na ",check4,"\n
        Entitie table no na ",check5,"\n
+       Sample IDs have valid names ", check6, "\n
        ")
      })
     }
@@ -362,19 +379,19 @@ server <- function(input,output,session){
       if(isTruthy(input$data_sample_anno1)){
         data_input[[input$omicType]] <- list(
           type=as.character(input$omicType),
-          Matrix=read.csv(
+          Matrix = read.csv(
             file = input$data_matrix1$datapath,
             header = T,
             row.names = 1,
             check.names = F
             ),
-          sample_table <- read.csv(
+          sample_table = read.csv(
             file = input$data_sample_anno1$datapath,
             header = T,
             row.names = 1,
             check.names = F
             ),
-          annotation_rows <- read.csv(
+          annotation_rows = read.csv(
             file = input$data_row_anno1$datapath,
             header = T,
             row.names = 1,

program/shinyApp/ui.R

@@ -34,6 +34,7 @@ library(zip)
 library(cicerone)
 library(shinyalert)
 library(msigdbr)
+library(tidyr)
 # library(svglite)
 
 source("R/C.R")