0202_2ed

.gitignore

@@ -5,5 +5,6 @@
 # dir
 /Input
 /Output
+/Log
 /图片
 /rsconnect

Modules/DrugOmicPair.R

@@ -136,7 +136,7 @@ serverDrugOmicPair <- function(input, output, session){
  }
  p_list <- p_list[!sapply(p_list, is.null)]
  # Warning 
- validate(
+ shiny::validate(
  need(length(p_list) > 0, "You have not chosen yet, or there is no result for this drug-omic pair.")
  )
  p <- wrap_plots(p_list, ncol = 3)

Modules/FeatureAcrossType.R

@@ -76,7 +76,7 @@ serverFeatureAcrossType <- function(input, output, session){
  # Preprocess
  select_features <- input$select_features
  if(select_features == "mRNA") select_features <- "exp"
- profile <- base::get(paste0(x, "_", select_features), envir = globalenv())
+ profile <- base::get(paste0(x, "_", select_features), envir = parent.env(environment()))
  intersected_cells <- intersect(cell_anno$Name, colnames(profile))
  sel_profile <- profile[rownames(profile) %in% input$select_specific_feature,
  match(intersected_cells, colnames(profile))]
@@ -158,7 +158,7 @@ serverFeatureAcrossType <- function(input, output, session){
  }
  p_list <- p_list[!sapply(p_list, is.null)]
  # Warning 
- validate(
+ shiny::validate(
  need(length(p_list) > 0, "You have not chosen yet, or there is no result for this feature.")
  )
  if(length(p_list) > 1){

Modules/FeatureDatabaseSig_singlethread.R

@@ -90,10 +90,10 @@ serverFeatureDatabaseSig <- function(input, output, session){
  # Prepare
  select_features1_2 <- input$select_features1
  if(select_features1_2 == "mRNA") select_features1_2 <- "exp"
- profile1 <- base::get(paste0(profile_comb[index,1], "_", select_features1_2), envir = globalenv())
+ profile1 <- base::get(paste0(profile_comb[index,1], "_", select_features1_2), envir = parent.env(environment()))
  select_features2_2 <- input$select_features2
  if(select_features2_2 == "mRNA") select_features2_2 <- "exp"
- profile2 <- base::get(paste0(profile_comb[index,2], "_", select_features2_2), envir = globalenv())
+ profile2 <- base::get(paste0(profile_comb[index,2], "_", select_features2_2), envir = parent.env(environment()))
  # Select specific feature and all features data
  # con vs con ----
  if(input$select_features1 %in% c("drug", "cnv",
@@ -265,7 +265,7 @@ serverFeatureDatabaseSig <- function(input, output, session){
  re_list[[index]] <- re
  incProgress(1/nrow(profile_comb), detail = paste0("Doing part ", index, "(Total ", nrow(profile_comb), ")"))
  # Warning 
- validate(
+ shiny::validate(
  need(length(profile_comb) > 0, "You have not chosen yet, or there is no result for this feature-database pair.")
  )
  }
@@ -283,7 +283,7 @@ serverFeatureDatabaseSig <- function(input, output, session){
  x$fea
  })
  # Warning 
- validate(
+ shiny::validate(
  need(length(re_name_list1) > 0, "You have not chosen yet, or there is no result for this feature-database pair.")
  )
  # message(class(re_list()))
@@ -311,7 +311,7 @@ serverFeatureDatabaseSig <- function(input, output, session){
  # Result Table ----
  output$re_table <- DT::renderDataTable({
  re_df <- do.call(rbind, re_list())
- validate(
+ shiny::validate(
  need(length(re_df) > 0, "You have not chosen yet, or there is no result for this feature-database pair.")
  )
  rownames(re_df) <- NULL

readme.md

@@ -1,6 +1,8 @@
 # OmicsPharDB
 A database that includes the largest published studies investigating the cancer cell lines to chemical compound treatment, and the association between drug sensitivity and multi-omics.
 
+
+
 # Contact with me
 
 Feel free to talk with me if you find any bugs or have any suggestions. :)