@sjcrh/proteinpaint-server 2.37.0 → 2.38.1

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/hclust.R

@@ -0,0 +1,125 @@
+# Usage:
+# time Rscript hclust.R in.json
+
+# Image is in Rplots.pdf
+
+############################
+#      !!! NOTE !!!        #
+############################
+# must not auto-install missing package in any R script!
+# declare required packages in dockerfile
+# at 2023/12, a problem emerged for pp container running in gdc qa-pink
+# 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
+
+# To plot the heatmap uncomment line `library(ggplot2) and lines after "Visualization" comment
+
+
+
+suppressPackageStartupMessages(library(dendextend))
+library(jsonlite)
+#library(flashClust)
+library(dendextend)
+library(reshape)
+#library(ggplot2) # Uncomment this line to plot heatmap in R 
+
+# Distance matrix
+args <- commandArgs(trailingOnly = T)
+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
+#}
+
+#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(input$matrix, method = "euclidean") # Transposing the matrix
+
+
+# Hierarchical clustering
+RowDend <- hclust(RowDist, method = tolower(input$cluster_method))
+#RowDend <- flashClust(RowDist, method = tolower(input$cluster_method))
+RowDendro <- as.dendrogram(RowDend)
+
+row_node_coordinates <- get_nodes_xy(
+  RowDendro,
+  type = "rectangle"
+)
+
+row_node_df <- as.data.frame(row_node_coordinates)
+colnames(row_node_df) <- c("x","y")
+
+# For columns (i.e samples)
+ColumnDist <- dist(t(input$matrix), method = "euclidean") # Transposing the matrix
+
+# Hierarchical clustering
+
+ColumnDend <- hclust(ColumnDist, method = tolower(input$cluster_method))
+#ColumnDend <- flashClust(ColumnDist,method = tolower(input$cluster_method))
+ColumnDendro <- as.dendrogram(ColumnDend)
+#plot (ColumnDendro)
+
+#print ("ColumnCoordinates")
+col_node_coordinates <- get_nodes_xy(
+  ColumnDendro,
+  type = "rectangle"
+)
+
+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]
+SortedRowNames <- input$row_names[RowDend$order]
+SortedColumnNames <- input$col_names[ColumnDend$order]
+
+#m <- matrix(SortedMatrix,length(SortedRowNames),length(SortedColumnNames))
+#colnames(m) <- SortedColumnNames
+#rownames(m) <- SortedRowNames
+
+output_df <- list()
+output_df$method <- input$cluster_method
+output_df$RowNodeJson <- row_node_df
+output_df$ColNodeJson <- col_node_df
+
+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
+
+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
+toJSON(output_df)
+
+
+# Visualization of heatmap, uncomment code below to get ggplot2 image of heatmap
+
+#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")
+

package/utils/fastclust.R

@@ -1,164 +0,0 @@
-# Usage:
-# time Rscript fastclust.R in.json
-
-# Image is in Rplots.pdf
-
-############################
-#      !!! NOTE !!!        #
-############################
-# must not auto-install missing package in any R script!
-# declare required packages in dockerfile
-# at 2023/12, a problem emerged for pp container running in gdc qa-pink
-# 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/')
-#}
-
-#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)
-
-# Distance matrix
-args <- commandArgs(trailingOnly = T)
-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
-}
-
-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
-
-
-# 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)
-#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,
-  type = "rectangle"
-)
-print ("RowCoordinates")
-print (row_node_coordinates)
-
-# For columns (i.e samples)
-ColumnDist <- dist(t(normalized_matrix), method = "euclidean") # Transposing the matrix
-
-# Hierarchical clustering
-
-ColumnDend <- hclust(ColumnDist, method = tolower(input$cluster_method))
-#ColumnDend <- flashClust(ColumnDist,method = tolower(input$cluster_method))
-ColumnDendro <- as.dendrogram(ColumnDend)
-#plot (ColumnDendro)
-
-col_node_coordinates <- get_nodes_xy(
-  ColumnDendro,
-  type = "rectangle"
-)
-print ("ColumnCoordinates")
-print (col_node_coordinates)
-
-print ("Done")
-# Sorting the matrix
-
-SortedMatrix  <- normalized_matrix[RowDend$order, ColumnDend$order]
-SortedRowNames <- rownames(normalized_matrix)[RowDend$order]
-SortedColumnNames <- colnames(normalized_matrix)[ColumnDend$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.
-
-
-#df  <- melt(m)
-#colnames(df) <- c("Genes", "Samples", "value")
-
-#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))
-
-#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()