From 766cf52f2aa3dfbe09977939269fbaee283f9ac5 Mon Sep 17 00:00:00 2001
From: Lea Seep <74967328+LeaSeep@users.noreply.github.com>
Date: Fri, 25 Nov 2022 09:20:06 +0100
Subject: [PATCH] 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 |  2 +-
 program/shinyApp/server.R       | 35 ++++++++++++++++++++++++---------
 program/shinyApp/ui.R           |  1 +
 3 files changed, 28 insertions(+), 10 deletions(-)

diff --git a/program/shinyApp/R/pca/server.R b/program/shinyApp/R/pca/server.R
index 2a123800..30d7929d 100644
--- a/program/shinyApp/R/pca/server.R
+++ b/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$loading)
         global_min <- -global_max
diff --git a/program/shinyApp/server.R b/program/shinyApp/server.R
index e2d7434c..1c62a644 100644
--- a/program/shinyApp/server.R
+++ b/program/shinyApp/server.R
@@ -230,8 +230,14 @@ server <- function(input,output,session){
        file = input$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
@@ -288,6 +295,15 @@ 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$OverallChecks <- renderText({
        paste0("Some overall Checks are running run ...\n
        Rownames of Matrix are the same as rownames of entitie table ",check1,"\n
@@ -295,6 +311,7 @@ server <- function(input,output,session){
        Matrix has no na ",check3,"\n
        Sample table no na ",check4,"\n
        Entitie table no na ",check5,"\n
+       Sample IDs have valid names ", check6, "\n
        ")
      })
     }
@@ -362,19 +379,19 @@ server <- function(input,output,session){
       if(isTruthy(input$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,
diff --git a/program/shinyApp/ui.R b/program/shinyApp/ui.R
index 25ee0d99..9af7adbd 100644
--- a/program/shinyApp/ui.R
+++ b/program/shinyApp/ui.R
@@ -34,6 +34,7 @@ library(zip)
 library(cicerone)
 library(shinyalert)
 library(msigdbr)
+library(tidyr)
 # library(svglite)
 
 source("R/C.R")