From a3d4a17458184f4b10d2ae5669ceefff82f3b837 Mon Sep 17 00:00:00 2001
From: Arash Bagherabadi <127447384+arashbioinfo@users.noreply.github.com>
Date: Mon, 19 Aug 2024 02:18:15 +0330
Subject: [PATCH] Create CircosPlot.R

---
 Plots/CircosPlot.R | 151 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 151 insertions(+)
 create mode 100644 Plots/CircosPlot.R

diff --git a/Plots/CircosPlot.R b/Plots/CircosPlot.R
new file mode 100644
index 0000000..6616a17
--- /dev/null
+++ b/Plots/CircosPlot.R
@@ -0,0 +1,151 @@
+# Install required packages
+#install.packages("readxl")
+#install.packages("circlize")
+#install.packages("ComplexHeatmap")
+library(readxl)
+library(circlize)
+library(ComplexHeatmap)
+
+# Set the working directory
+dir <- "E:/0Projects/CircosPlot"
+setwd(dir)
+
+# Set scipen to a high value to prevent scientific notation
+set.seed(42)
+options(scipen = 999)
+
+# Read the Excel file
+DEL <- as.data.frame(read_excel("NEW v5_complete.xlsx", sheet = 2))
+DUP <- as.data.frame(read_excel("NEW v5_complete.xlsx", sheet = 3)) 
+INV <- as.data.frame(read_excel("NEW v5_complete.xlsx", sheet = 4)) 
+OTHER <- as.data.frame(read_excel("NEW v5_complete.xlsx", sheet = 5)) 
+TRA <- as.data.frame(read_excel("NEW v5_complete.xlsx", sheet = 6))
+
+# Define colors for each sample type
+sample_colors <- c("ALL" = "#0080FF", "AML" = "#00994C", "CLL" = "#FF0000",
+                   "MDS" = "#CC00CC", "Prenatal" = "#404040")
+
+# Define shapes for each technology type
+tech_shapes <- c("SOC" = 17, "SOC&OGM" = 16, "OGM" = 15) # 16: circle, 17: triangle, 18: square
+
+# GENERATE the plot
+pdf("plot_with_legends.pdf", width = 20 , height = 20)
+
+# Initialize circos plot with extra space for legends
+circos.par("start.degree" = 90,
+           "gap.degree" = c(rep(2,23),3),
+           "canvas.xlim" = c(-1.5, 1.5),
+           "canvas.ylim" = c(-1.5, 1.5))
+
+
+circos.initializeWithIdeogram(species = "hg19")
+
+# Add genomic tracks with points colored by type and shaped by tech
+circos.genomicTrackPlotRegion(DEL, 
+  panel.fun = function(region, value, ...) {
+  col <- sample_colors[value$type]
+  pch <- tech_shapes[value$tech]
+  circos.genomicPoints(region, value, col = col, pch = pch, cex = 0.8, ...)},
+  track.height = 0.08, # Set the track height
+  ylim = c(0, 1),
+  bg.border = NA,   # No border
+  bg.col = "gray95" # Light gray background
+  )
+
+
+DUP <- na.omit(DUP)
+circos.genomicTrackPlotRegion(DUP, 
+  panel.fun = function(region, value, ...) {
+  col <- sample_colors[value$type]
+  pch <- tech_shapes[value$tech]
+  circos.genomicPoints(region, value, col = col, pch = pch, cex = 0.8, ...)},
+  track.height = 0.08, # Set the track height
+  ylim = c(0, 1),
+  bg.border = NA,   # No border
+  bg.col = "gray96" # Light gray background
+)
+
+circos.genomicTrackPlotRegion(INV, 
+  panel.fun = function(region, value, ...) {
+  col <- sample_colors[value$type]
+  pch <- tech_shapes[value$tech]
+  circos.genomicPoints(region, value, col = col, pch = pch, cex = 0.8, ...)},
+  track.height = 0.08, # Set the track height
+  ylim = c(0, 1),
+  bg.border = NA,   # No border
+  bg.col = "gray97" # Light gray background
+)
+
+circos.genomicTrackPlotRegion(OTHER, panel.fun = function(region, value, ...) {
+  col <- sample_colors[value$type]
+  pch <- tech_shapes[value$tech]
+  circos.genomicPoints(region, value, col = col, pch = pch, cex = 0.8, ...)},
+  track.height = 0.08, # Set the track height
+  ylim = c(0, 1),
+  bg.border = NA,   # No border
+  bg.col = "gray98" # Light gray background
+)
+
+TRA <- na.omit(TRA)
+for (i in 1:nrow(TRA)) {
+  type <- TRA$type[i]
+  tech <- TRA$tech[i]
+  col <- sample_colors[type]
+  lty_map <- c("SOC&OGM" = 1, "SOC" = 2, "OGM" = 3) # 1: solid, 2: dashed, 3: dotted
+  lty <- lty_map[tech]
+  
+  circos.link(
+    sector.index1 = TRA$from_chr[i], point1 = c(TRA$from_start[i], TRA$from_end[i]),
+    sector.index2 = TRA$to_chr[i], point2 = c(TRA$to_start[i], TRA$to_end[i]),
+    col = col, lty = lty , lwd = 1.5 #, border = NA
+  )
+}
+
+# Add track labels in the gap (4 degrees) vertically
+track_labels <- c("DELETION", "DUPLICATION", "INVERSION", "OTHER")
+#track_labels <- c("DELETION", "DUPLICATION", "INVERSION", "OTHER", "TRANSLOCATION")
+track_y_positions <- c(5, 3.5, 2, 0.5)
+
+for (i in seq_along(track_labels)) {
+  circos.text(x = 25, y = track_y_positions[i], labels = track_labels[i], 
+              sector.index = "chr1", facing = "clockwise", niceFacing = TRUE,
+              adj = c(0.5, -1), cex = 0.7, font = 2)
+}
+
+# Clear circos plot
+circos.clear()
+
+# Create legends
+sample_legend <- Legend(at = names(sample_colors), 
+                        type = "points", 
+                        legend_gp = gpar(col = sample_colors),
+                        title = "Sample Types")
+
+tech_legend <- Legend(at = names(tech_shapes), 
+                      type = "points", 
+                      legend_gp = gpar(col = "black"), 
+                      pch = tech_shapes,
+                      title = "Technology Types")
+
+line_types <- c("SOC&OGM" = "solid", "SOC" = "dashed", "OGM" = "dotted")
+
+line_legend <- Legend(at = names(line_types), 
+                      type = "lines", 
+                      legend_gp = gpar(lty = c(1, 2, 3), col = "black"),
+                      title = "Line Types")
+
+# Draw legends
+pushViewport(viewport(x = 1.35, y = 1.11, just = c("right", "top")))
+draw(sample_legend)
+upViewport()
+
+pushViewport(viewport(x = 1.355, y = 1.05, just = c("right", "top")))
+draw(tech_legend)
+upViewport()
+
+pushViewport(viewport(x = 1.35, y = 1, just = c("right", "top")))
+draw(line_legend)
+upViewport()
+
+dev.off()
+