add 删除R脚本中多余的图形绘制

res/heatmap_script.R

@@ -1,14 +1,11 @@
 # Load required packages
-suppressPackageStartupMessages(library(grid))
-suppressPackageStartupMessages(library(ComplexHeatmap))
 suppressPackageStartupMessages(library(circlize))
 suppressPackageStartupMessages(library(RColorBrewer))
+suppressPackageStartupMessages(library(ComplexHeatmap))
 suppressPackageStartupMessages(library(dendextend))
-suppressPackageStartupMessages(library(dendsort))
-suppressPackageStartupMessages(library(gridBase))
 
 # Get arguments from the command line
-args <- commandArgs(T)
+args <- commandArgs(trailingOnly = TRUE)
 
 # Check the number of arguments
 if (length(args) != 2) {
@@ -24,23 +21,17 @@ if (!file.exists(input_csv)) {
   stop("The input file does not exist. Please check the file path.", call. = FALSE)
 }
 
-# Load the data for plotting
+# Function to load and preprocess data
-data <- read.table(file = input_csv, header = TRUE, row.names = 1, sep = ',')
+load_and_preprocess_data <- function(file_path) {
+  data <- read.table(file = file_path, header = TRUE, row.names = 1, sep = ',')
+  data_matrix <- as.matrix(data)
+  normalized_data <- t(scale(t(data_matrix)))
+  normalized_data[is.na(normalized_data)] <- 0
+  return(normalized_data)
+}
 
-# View the data
+# Load and preprocess data
-message("Data loaded successfully. The first few rows are as follows:")
+cir1 <- load_and_preprocess_data(input_csv)
-print(head(data))
-
-# Convert to matrix format and normalize the data
-data <- as.matrix(data)
-cir1 <- t(scale(t(data)))
-
-# Handle NA values
-cir1[is.na(cir1)] <- 0
-
-# View the normalized data
-message("Data normalization successful. The first few rows are as follows:")
-print(head(cir1))
 
 # Define the color gradient for the heatmap
 mycol <- colorRamp2(c(-2.5, 0.3, 3.1), c("blue", "white", "red"))
@@ -48,57 +39,37 @@ mycol <- colorRamp2(c(-2.5, 0.3, 3.1), c("blue", "white", "red"))
 # Open the PDF device
 pdf(output_pdf, width = 10, height = 8)
 
-# Draw the basic circular heatmap
+# Draw the adjusted and beautified circular heatmap
-message("Drawing the basic circular heatmap...")
-circos.heatmap(cir1, col = mycol)
-circos.clear()
-
-# Adjust and beautify the circular heatmap in circos.heatmap()
-message("Drawing the adjusted and beautified circular heatmap...")
 circos.par(gap.after = c(30))
-circos.heatmap(cir1, col = mycol,
+circos.heatmap(cir1, 
-               dend.side = "inside",
+                col = mycol, 
-               rownames.side = "outside",
+                dend.side = "inside", 
-               rownames.col = "black",
+                rownames.side = "outside", 
-               rownames.cex = 1.2,
+                rownames.col = "black", 
-               rownames.font = 1.2,
+                rownames.cex = 1.3, 
-               bg.border = "black",
+                track.height = 0.35, 
-               cluster = TRUE)
+                cluster = TRUE, 
-circos.clear()
+                dend.track.height = 0.18, 
+                dend.callback = function(dend, m, si) {
+                  color_branches(dend, k = 15, col = 1:15)
+                })
 
-# Adjust and beautify the dendrogram
+# Add column names
-message("Drawing the circular heatmap with adjusted and beautified dendrogram...")
-circos.par(gap.after = c(30))
-circos.heatmap(cir1, col = mycol, dend.side = "inside",
-               rownames.side = "outside",
-               track.height = 0.35,
-               rownames.col = "black",
-               rownames.cex = 1.3,
-               rownames.font = 1.3,
-               cluster = TRUE,
-               dend.track.height = 0.18,
-               dend.callback = function(dend, m, si) {
-                 color_branches(dend, k = 15, col = 1:15)
-               })
-
-# 添加列名
 circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
   if (CELL_META$sector.numeric.index == 1) {
     cn <- colnames(cir1)
     n <- length(cn)
-    # Adjust the x and y positions
     circos.text(rep(CELL_META$cell.xlim[2], n) + convert_x(0.5, "mm"), 
                 1:n + 2.5, 
                 cn, cex = 0.6, adj = c(0, 0.5), facing = "inside")
   }
 }, bg.border = NA)
 
-# 添加图例
+# Add legend
-message("Adding legend labels...")
 lg <- Legend(title = "Exp", col_fun = mycol, direction = "vertical")
 grid.draw(lg)
 
-# 清除环形图
+# Clear the circular plot
 circos.clear()
 
 # Close the PDF device