get Hmisc::rcorr results properly

microbiomeDB · Nov 30, 2023 · 5ddf460 · 5ddf460
1 parent 7360be2
commit 5ddf460
Showing 1 changed file with 10 additions and 6 deletions.
diff --git a/R/server.R b/R/server.R
@@ -38,12 +38,16 @@ server <- function(input, output, session) {
         data2 <- readData(file2)
       }
 
-      numData1Cols <- length(data1)
-      numData2Cols <- length(data2)
-
-      corrData <- Hmisc::rcorr(as.matrix(data1), as.matrix(data2))
-      pValuesMatrix$p_values <- corrData$P[1:numData1Cols, 1:numData2Cols]
-      correlationMatrix$corr_matrix <- corrData$r[1:numData1Cols, 1:numData2Cols]
+      lastData1ColIndex <- length(data1)
+      firstData2ColIndex <- length(data1) + 1
+      corrResult <- Hmisc::rcorr(as.matrix(data1), as.matrix(data2))
+      print(corrResult)
+      # this bc Hmisc::rcorr cbinds the two data.tables and runs the correlation
+      # so we need to extract only the relevant values
+      pValuesMatrix$p_values <- corrResult$P[1:lastData1ColIndex, firstData2ColIndex:length(colnames(corrResult$P))]
+      print(pValuesMatrix$p_values)
+      correlationMatrix$corr_matrix <- corrResult$r[1:lastData1ColIndex, firstData2ColIndex:length(colnames(corrResult$r))]
+      print(correlationMatrix$corr_matrix)
     }, error = function(e) {
       shiny::showNotification(paste('Error:', e$message), type = 'error')
     })