@sjcrh/proteinpaint-server 2.37.0 → 2.38.0

package/utils/cuminc.R

@@ -201,10 +201,9 @@ runPermutations <- function(M, dat) {
 # function to compute p-value for permutation test
 # perform two-tailed test
 getPermutePvalue <- function(tsPs, tsO) {
-  B_left <- sum(tsPs <= -abs(tsO))
-  B_right <- sum(tsPs >= abs(tsO))
-  B <- B_left + B_right
-  pvalue <- signif((B+1)/(length(tsPs)+1), 2)
+  P_left <- sum(tsPs <= -abs(tsO))/(length(tsPs)+1)
+  P_right <- sum(tsPs >= abs(tsO))/(length(tsPs)+1)
+  pvalue <- signif(P_left + P_right, 2)
   return(pvalue)
 }
 

package/utils/{fastclust.R → hclust.R}

@@ -1,5 +1,5 @@
 # Usage:
-# time Rscript fastclust.R in.json
+# time Rscript hclust.R in.json
 
 # Image is in Rplots.pdf
 
@@ -68,7 +68,6 @@ RowDist <- dist(normalized_matrix, method = "euclidean") # Transposing the matri
 
 
 # Hierarchical clustering
-print (input$cluster_method)
 RowDend <- hclust(RowDist, method = tolower(input$cluster_method))
 #RowDend <- flashClust(RowDist, method = tolower(input$cluster_method))
 #print (RowDend$order)
@@ -93,8 +92,19 @@ row_node_coordinates <- get_nodes_xy(
   RowDendro,
   type = "rectangle"
 )
-print ("RowCoordinates")
-print (row_node_coordinates)
+
+row_node_df <- as.data.frame(row_node_coordinates)
+colnames(row_node_df) <- c("x","y")
+
+#row_node_transform <- apply(row_node_coordinates, 1, function(row){
+#    lapply(c(1,2), function(col_index){
+#        if (col_index == 1) {
+#          list(x=row[col_index])
+#        } else if (col_index == 2) {
+#          list(y=row[col_index])
+#        }
+#    })
+#})
 
 # For columns (i.e samples)
 ColumnDist <- dist(t(normalized_matrix), method = "euclidean") # Transposing the matrix
@@ -106,14 +116,15 @@ ColumnDend <- hclust(ColumnDist, method = tolower(input$cluster_method))
 ColumnDendro <- as.dendrogram(ColumnDend)
 #plot (ColumnDendro)
 
+#print ("ColumnCoordinates")
 col_node_coordinates <- get_nodes_xy(
   ColumnDendro,
   type = "rectangle"
 )
-print ("ColumnCoordinates")
-print (col_node_coordinates)
 
-print ("Done")
+col_node_df <- as.data.frame(col_node_coordinates)
+colnames(col_node_df) <- c("x","y")
+
 # Sorting the matrix
 
 SortedMatrix  <- normalized_matrix[RowDend$order, ColumnDend$order]
@@ -123,11 +134,52 @@ SortedColumnNames <- colnames(normalized_matrix)[ColumnDend$order]
 #m <- matrix(SortedMatrix,length(SortedRowNames),length(SortedColumnNames))
 #colnames(m) <- SortedColumnNames
 #rownames(m) <- SortedRowNames
-cat("rowindexes",RowDend$order,"\n",sep="\t") # Prints out row indices
-cat("colindexes",ColumnDend$order,"\n",sep="\t") # Prints out column indicies
-cat("rownames",SortedRowNames,"\n",sep="\t") # Prints out row names
-cat("colnames",SortedColumnNames,"\n",sep="\t") # Prints out column names
-cat ("OutputMatrix",normalized_matrix,"\n",sep="\t") # This outputs the 2D array in 1D column-wise. This is later converted to 2D array in nodejs.
+
+output_df <- list()
+output_df$method <- input$cluster_method
+output_df$RowNodeJson <- row_node_df
+output_df$ColNodeJson <- col_node_df
+#output_df$RowDendOrder <- {lapply(1:length(RowDend$order), function(y){
+#    list(i=RowDend$order[y])
+#})}
+row_dend_order_df <- as.data.frame(RowDend$order)
+colnames(row_dend_order_df) <- c("ind")
+output_df$RowDendOrder <- row_dend_order_df
+
+col_dend_order_df <- as.data.frame(ColumnDend$order)
+colnames(col_dend_order_df) <- c("ind")
+output_df$ColumnDendOrder <- col_dend_order_df
+
+#output_df$SortedRowNames <- {lapply(1:length(SortedRowNames), function(y){
+#    list(gene=SortedRowNames[y])
+#})}
+
+sorted_row_names_df <- as.data.frame(SortedRowNames)
+colnames(sorted_row_names_df) <- c("gene")
+output_df$SortedRowNames <- sorted_row_names_df
+
+sorted_col_names_df <- as.data.frame(SortedColumnNames)
+colnames(sorted_col_names_df) <- c("sample")
+output_df$SortedColumnNames <- sorted_col_names_df
+
+output_df$OutputMatrix <- {lapply(1:length(normalized_matrix), function(y){
+    list(elem=normalized_matrix[y])
+})}
+
+# Converting to data frame does not work for the raw counts since the key of the json needs to be unique.
+
+#output_matrix_df <- as.data.frame(normalized_matrix)
+#colnames(output_matrix_df) <- c(rep("elem",dim(normalized_matrix)[2]))
+#print (output_matrix_df)
+#output_df$OutputMatrix <- output_matrix_df
+
+toJSON(output_df)
+
+#cat("rowindexes",RowDend$order,"\n",sep="\t") # Prints out row indices
+#cat("colindexes",ColumnDend$order,"\n",sep="\t") # Prints out column indicies
+#cat("rownames",SortedRowNames,"\n",sep="\t") # Prints out row names
+#cat("colnames",SortedColumnNames,"\n",sep="\t") # Prints out column names
+#cat ("OutputMatrix",normalized_matrix,"\n",sep="\t") # This outputs the 2D array in 1D column-wise. This is later converted to 2D array in nodejs.
 
 
 #df  <- melt(m)