removed expr_data from all code -- it is not needed now that PCA and …

…pheatmap use data_long
jminnier · Nov 3, 2016 · 73afd55 · 73afd55
1 parent 6db42bf
commit 73afd55
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Showing 4 changed files with 7 additions and 11 deletions.
diff --git a/helpers.R b/helpers.R
@@ -59,7 +59,7 @@ if(FALSE) {
   load('data/mousecounts_example_analyzed.RData') #example_data_results
   data_analyzed = list('group_names'=group_names,'sampledata'=sampledata,
                        "results"=results,"data_long"=data_long, "geneids"=geneids,
-                       "expr_data"=expr_data,"data_results_table"=example_data_results)
+                       "data_results_table"=example_data_results)
 
   data_results = data_analyzed$results
 

diff --git a/save_example_data.R b/save_example_data.R
@@ -157,7 +157,7 @@ data = countdata
 results = lmobj_res
 
 #after running analysis pipeline, export this code to another example construction file
-save(countdata,group_names,sampledata,results,data_long,geneids,expr_data,
+save(countdata,group_names,sampledata,results,data_long,geneids,
      file="data/mousecounts_example_analysis_results.RData")
 
 

diff --git a/server-inputdata.R b/server-inputdata.R
@@ -114,7 +114,7 @@ analyzeDataReactive <-
                       load('data/mousecounts_example_analyzed.RData') #example_data_results for data_results_table
                       return(list('group_names'=group_names,'sampledata'=sampledata,
                                   "results"=results,"data_long"=data_long, "geneids"=geneids,
-                                  "expr_data"=expr_data,"data_results_table"=example_data_results))
+                                  "data_results_table"=example_data_results))
                     }
 
                     ## ==================================================================================== ##
@@ -127,7 +127,7 @@ analyzeDataReactive <-
 
                       return(list('group_names'=group_names,'sampledata'=sampledata,
                                   "results"=results,"data_long"=data_long, 
-                                  "geneids"=geneids, "expr_data"=expr_data,
+                                  "geneids"=geneids,
                                   "data_results_table"=data_results_table))
                     }
 
@@ -259,7 +259,7 @@ analyzeDataReactive <-
 
                       return(list('group_names'=group_names,'sampledata'=sampledata,
                                   "results"=tmpres,"data_long"=data_long, 
-                                  "geneids"=geneids,"expr_data"=expr_data,
+                                  "geneids"=geneids,
                                   "data_results_table"=alldata))
                     }else if(input$inputdat_type=="expression_only") {
 
@@ -395,14 +395,11 @@ analyzeDataReactive <-
                         data_long = data_long%>%select(-one_of(tmpgeneidnames))
                       }
 
-                      #expr_data = tmplog2cpm[,-1]
-
                       print('analyze data: done')
 
 
                       return(list('group_names'=group_names,'sampledata'=sampledata,
                                   "results"=lmobj_res,"data_long"=data_long, "geneids"=geneids, 
-                                  "expr_data"=expr_data,
                                   "data_results_table"=data_results_table))
 
                     }     
@@ -452,11 +449,10 @@ output$downloadResults_RData <- downloadHandler(filename= paste0("START_results_
                                                   results = tmp$results
                                                   data_long = tmp$data_long
                                                   geneids = tmp$geneids
-                                                  expr_data = tmp$expr_data
                                                   data_results_table = tmp$data_results_table
 
                                                   save(group_names,sampledata,results,
-                                                       data_long,geneids,expr_data,
+                                                       data_long,geneids,
                                                        data_results_table,file=file)
                                                 })
 

diff --git a/server-samplegroupplots.R b/server-samplegroupplots.R
@@ -37,7 +37,7 @@ observe({
   print("server-samplegroupplots-update-groups")
   data_analyzed = analyzeDataReactive()
   tmpgroups = data_analyzed$group_names
-  tmpsamples = colnames(data_analyzed$expr_data) 
+  tmpsamples = as.character(data_analyzed$sampledata$sampleid)
   updateSelectizeInput(session,'sampleres_groups',
                        choices=tmpgroups, selected=tmpgroups)
   updateSelectizeInput(session,'sampleres_samples',