@sjcrh/proteinpaint-server 2.14.4 → 2.16.0

package/shared/common.js

@@ -472,7 +472,8 @@ export const tkt = {
 	mds2: 'mds2', // mds 2nd gen
 	mds3: 'mds3', // 3rd gen
 	bedgraphdot: 'bedgraphdot',
-	bam: 'bam'
+	bam: 'bam',
+	ld: 'ld'
 }
 
 export function validtkt(what) {

package/utils/fastclust.R

@@ -0,0 +1,129 @@
+# Usage:
+# time Rscript fastclust.R in.json
+
+# Image is in Rplots.pdf
+
+# Checking if all R packages are installed or not, if not installing each one of them
+
+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)
+
+# For columns (i.e samples)
+RowDist <- dist(input$matrix, method = "euclidean") # Transposing the matrix
+
+# Hierarchical clustering
+print (input$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$call)
+#print ("Attributes")
+#attributes(RowDend)
+#print ("methods")
+#methods(class=class(RowDend))
+RowDendro <- as.dendrogram(RowDend)
+#print ("Attributes as.dendrogram")
+#attributes(RowDendro)
+plot(RowDendro)
+
+node_coordinates <- get_nodes_xy(
+  RowDendro,
+  type = "rectangle"
+)
+print (node_coordinates)
+
+# For columns (i.e samples)
+ColumnDist <- dist(t(input$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)
+
+# Sorting the matrix
+
+SortedMatrix  <- input$matrix[RowDend$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
+
+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")
+
+#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()

package/utils/lowess.R

@@ -0,0 +1,9 @@
+library(jsonlite)
+
+# read in data
+args <- commandArgs(trailingOnly = T)
+if (length(args) != 1) stop("input coordinates needed")
+infile <- args[1]
+data <- fromJSON(infile)
+result = lowess(data$X, data$Y)
+toJSON(result)

package/server.js.LICENSE.txt

@@ -1 +0,0 @@
-//!!! DO NOT USE FOR geneVariant filterCTE constructor