109 lines
3.3 KiB
R
109 lines
3.3 KiB
R
# Load required packages
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suppressPackageStartupMessages(library(grid))
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suppressPackageStartupMessages(library(ComplexHeatmap))
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suppressPackageStartupMessages(library(circlize))
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suppressPackageStartupMessages(library(RColorBrewer))
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suppressPackageStartupMessages(library(dendextend))
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suppressPackageStartupMessages(library(dendsort))
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suppressPackageStartupMessages(library(gridBase))
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# Get arguments from the command line
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args=commandArgs(T);
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# Check the number of arguments
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if (length(args) != 2) {
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stop("Please provide two arguments: the input CSV file path and the output PDF file path.", call. = FALSE)
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}
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# Get the input CSV file path and the output PDF file path
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input_csv <- args[1]
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output_pdf <- args[2]
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# Check if the input file exists
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if (!file.exists(input_csv)) {
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stop("The input file does not exist. Please check the file path.", call. = FALSE)
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}
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# Load the data for plotting
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data <- read.table(file = input_csv, header = TRUE, row.names = 1, sep = ',')
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# View the data
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message("Data loaded successfully. The first few rows are as follows:")
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print(head(data))
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# Convert to matrix format and normalize the data
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data <- as.matrix(data)
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cir1 <- t(scale(t(data)))
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# Handle NA values
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cir1[is.na(cir1)] <- 0
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# View the normalized data
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message("Data normalization successful. The first few rows are as follows:")
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print(head(cir1))
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# Define the color gradient for the heatmap
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mycol <- colorRamp2(c(-2.5, 0.3, 3.1), c("blue", "white", "red"))
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# Open the PDF device
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pdf(output_pdf, width = 10, height = 8)
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# Draw the basic circular heatmap
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message("Drawing the basic circular heatmap...")
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circos.heatmap(cir1, col = mycol)
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circos.clear()
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# Adjust and beautify the circular heatmap in circos.heatmap()
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message("Drawing the adjusted and beautified circular heatmap...")
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circos.par(gap.after = c(30))
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circos.heatmap(cir1, col = mycol,
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dend.side = "inside",
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rownames.side = "outside",
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rownames.col = "black",
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rownames.cex = 1.2,
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rownames.font = 1.2,
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bg.border = "black",
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cluster = TRUE)
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circos.clear()
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# Adjust and beautify the dendrogram
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message("Drawing the circular heatmap with adjusted and beautified dendrogram...")
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circos.par(gap.after = c(30))
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circos.heatmap(cir1, col = mycol, dend.side = "inside",
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rownames.side = "outside",
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track.height = 0.28,
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rownames.col = "black",
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rownames.cex = 1.3,
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rownames.font = 1.3,
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cluster = TRUE,
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dend.track.height = 0.18,
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dend.callback = function(dend, m, si) {
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color_branches(dend, k = 15, col = 1:15)
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})
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circos.clear()
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# Add legend labels
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message("Adding legend labels...")
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lg <- Legend(title = "Exp", col_fun = mycol,
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direction = c("vertical"))
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grid.draw(lg)
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# Add column names
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message("Adding column names...")
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circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
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if (CELL_META$sector.numeric.index == 1) {
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cn <- colnames(cir1)
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n <- length(cn)
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circos.text(rep(CELL_META$cell.xlim[2], n) + convert_x(0.5, "mm"),
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1:n + 5,
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cn, cex = 0.6, adj = c(0, 0.5), facing = "inside")
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}
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}, bg.border = NA)
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circos.clear()
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# Close the PDF device
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dev.off()
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message("The heatmap has been successfully saved to: ", output_pdf)
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