@sjcrh/proteinpaint-server 2.38.0 → 2.38.1

package/utils/hclust.R

@@ -12,37 +12,16 @@
 # since the docker images lacks the packages, but the auto-install was prevented due to container safety (no internet query)
 # this script will not run, leading to hard to decipher crashing
 
-#ggplot2_path <- system.file(package='ggplot2')
-#if (nchar(ggplot2_path) == 0) {
-#  install.packages("ggplot2", repos='https://cran.case.edu/')
-#}
-#
-#jsonlite_path <- system.file(package='jsonlite')
-#if (nchar(jsonlite_path) == 0) {
-#  install.packages("jsonlite", repos='https://cran.case.edu/')
-#}
-#
-#dendextend_path <- system.file(package='dendextend')
-#if (nchar(dendextend_path) == 0) {
-#  install.packages("dendextend", repos='https://cran.case.edu/')
-#}
-#
-#reshape_path <- system.file(package='reshape')
-#if (nchar(reshape_path) == 0) {
-#  install.packages("reshape", repos='https://cran.case.edu/')
-#}
+# To plot the heatmap uncomment line `library(ggplot2) and lines after "Visualization" comment
+
 
-#flashClust_path <- system.file(package='flashClust')
-#if (nchar(flashClust_path) == 0) {
-#  install.packages("flashClust", repos='https://cran.case.edu/')
-#}
 
 suppressPackageStartupMessages(library(dendextend))
 library(jsonlite)
 #library(flashClust)
 library(dendextend)
 library(reshape)
-library(ggplot2)
+#library(ggplot2) # Uncomment this line to plot heatmap in R 
 
 # Distance matrix
 args <- commandArgs(trailingOnly = T)
@@ -50,43 +29,27 @@ if (length(args) != 1) stop("Usage: Rscript test.R in.json > results")
 infile <- args[1]
 input <- fromJSON(infile)
 
-if (length(input$valueIsTransformed) == 0 || input$valueIsTransformed == FALSE) {
- normalized_matrix <- t(scale(t(input$matrix))) # Applying z-score normalization
-} else { # No normalization
- normalized_matrix <- input$matrix
-}
+#if (length(input$valueIsTransformed) == 0 || input$valueIsTransformed == FALSE) {
+# normalized_matrix <- t(scale(t(input$matrix))) # Applying z-score normalization
+#} else { # No normalization
+# normalized_matrix <- input$matrix
+#}
 
-rownames(normalized_matrix) <- input$row_names
-colnames(normalized_matrix) <- input$col_names
-normalized_matrix <- na.omit(normalized_matrix) # Removes rows with NA values
+#rownames(normalized_matrix) <- input$row_names
+#colnames(normalized_matrix) <- input$col_names
+#normalized_matrix <- na.omit(normalized_matrix) # Removes rows with NA values
 
 #print ("normalized_matrix")
 #print (dim(normalized_matrix))
 
 # For columns (i.e samples)
-RowDist <- dist(normalized_matrix, method = "euclidean") # Transposing the matrix
+RowDist <- dist(input$matrix, method = "euclidean") # Transposing the matrix
 
 
 # Hierarchical clustering
 RowDend <- hclust(RowDist, method = tolower(input$cluster_method))
 #RowDend <- flashClust(RowDist, method = tolower(input$cluster_method))
-#print (RowDend$order)
-#print ("Merge")
-#print (RowDend$merge)
-#print ("Height")
-#print (RowDend$height)
-#print ("Labels")
-#print (RowDend$labels)
-#print ("Calls")
-#print (RowDend$call)
-#print ("Attributes")
-#attributes(RowDend)
-#print ("methods")
-#methods(class=class(RowDend))
 RowDendro <- as.dendrogram(RowDend)
-#print ("Attributes as.dendrogram")
-#attributes(RowDendro)
-#plot(RowDendro)
 
 row_node_coordinates <- get_nodes_xy(
   RowDendro,
@@ -96,18 +59,8 @@ row_node_coordinates <- get_nodes_xy(
 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
+ColumnDist <- dist(t(input$matrix), method = "euclidean") # Transposing the matrix
 
 # Hierarchical clustering
 
@@ -127,9 +80,9 @@ colnames(col_node_df) <- c("x","y")
 
 # Sorting the matrix
 
-SortedMatrix  <- normalized_matrix[RowDend$order, ColumnDend$order]
-SortedRowNames <- rownames(normalized_matrix)[RowDend$order]
-SortedColumnNames <- colnames(normalized_matrix)[ColumnDend$order]
+#SortedMatrix  <- normalized_matrix[RowDend$order, ColumnDend$order]
+SortedRowNames <- input$row_names[RowDend$order]
+SortedColumnNames <- input$col_names[ColumnDend$order]
 
 #m <- matrix(SortedMatrix,length(SortedRowNames),length(SortedColumnNames))
 #colnames(m) <- SortedColumnNames
@@ -139,9 +92,7 @@ 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$RowDendOrder <- row_dend_order_df
@@ -150,10 +101,6 @@ col_dend_order_df <- as.data.frame(ColumnDend$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
@@ -161,56 +108,18 @@ 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)
-#colnames(df) <- c("Genes", "Samples", "value")
+# Visualization of heatmap, uncomment code below to get ggplot2 image of heatmap
 
-#ggplot(df, aes(x = Genes, y = Samples, fill = value)) + geom_tile() + scale_fill_gradient(low="blue", high="red") + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
+#SortedMatrix  <- input$matrix[RowDend$order, ColumnDend$order]
+#SortedRowNames <- rownames(input$matrix)[RowDend$order]
+#SortedColumnNames <- colnames(input$matrix)[ColumnDend$order]
+#
+#matrix_melt <- melt(SortedMatrix)
+#ggplot(data = matrix_melt, aes(x = X1, y = X2, fill = value)) +
+#  geom_tile() + scale_fill_gradient(low="blue", high="red")
 
 #ggsave("heatmap.png")
 
-
-##print (SortedMatrix)
-#df  <- as.data.frame(SortedMatrix)
-#rownames(df)  <- SortedRowNames
-#colnames(df)  <- SortedColumnNames
-#print ("DataFrame")
-#print (df)
-##plt <- ggplot(as.data.frame(SortedMatrix), aes(SortedColumnNames,SortedRowNames)) + geom_tile() + theme_minimal()
-#plt <- ggplot(df,aes(x=colname,y=rownames(df))) + geom_tile() + theme_minimal()
-#
-## setting gradient color as red and white
-#plt <- plt + scale_fill_gradient(low="blue", high="red")
-#
-## setting the title and subtitles using
-## title and subtitle
-#plt <- plt + labs(title = "Heatmap")
-#plt <- plt + labs(subtitle = "A simple heatmap using geom_tile()")
-#
-## setting x and y labels using labs
-#plt <- plt + labs(x ="Samples", y ="Genes")
-#
-## plotting the Heatmap
-#plt
-#png("heatmap.png")
-#dev.off()