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# Install required packages | ||
#install.packages("readxl") | ||
#install.packages("circlize") | ||
#install.packages("ComplexHeatmap") | ||
library(readxl) | ||
library(circlize) | ||
library(ComplexHeatmap) | ||
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# Set the working directory | ||
dir <- "E:/0Projects/CircosPlot" | ||
setwd(dir) | ||
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# Set scipen to a high value to prevent scientific notation | ||
set.seed(42) | ||
options(scipen = 999) | ||
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# 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)) | ||
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# Define colors for each sample type | ||
sample_colors <- c("ALL" = "#0080FF", "AML" = "#00994C", "CLL" = "#FF0000", | ||
"MDS" = "#CC00CC", "Prenatal" = "#404040") | ||
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# Define shapes for each technology type | ||
tech_shapes <- c("SOC" = 17, "SOC&OGM" = 16, "OGM" = 15) # 16: circle, 17: triangle, 18: square | ||
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# GENERATE the plot | ||
pdf("plot_with_legends.pdf", width = 20 , height = 20) | ||
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# 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)) | ||
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circos.initializeWithIdeogram(species = "hg19") | ||
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# 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 | ||
) | ||
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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 | ||
) | ||
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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 | ||
) | ||
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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 | ||
) | ||
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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] | ||
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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 | ||
) | ||
} | ||
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# 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) | ||
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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) | ||
} | ||
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# Clear circos plot | ||
circos.clear() | ||
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# Create legends | ||
sample_legend <- Legend(at = names(sample_colors), | ||
type = "points", | ||
legend_gp = gpar(col = sample_colors), | ||
title = "Sample Types") | ||
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tech_legend <- Legend(at = names(tech_shapes), | ||
type = "points", | ||
legend_gp = gpar(col = "black"), | ||
pch = tech_shapes, | ||
title = "Technology Types") | ||
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line_types <- c("SOC&OGM" = "solid", "SOC" = "dashed", "OGM" = "dotted") | ||
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line_legend <- Legend(at = names(line_types), | ||
type = "lines", | ||
legend_gp = gpar(lty = c(1, 2, 3), col = "black"), | ||
title = "Line Types") | ||
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# Draw legends | ||
pushViewport(viewport(x = 1.35, y = 1.11, just = c("right", "top"))) | ||
draw(sample_legend) | ||
upViewport() | ||
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pushViewport(viewport(x = 1.355, y = 1.05, just = c("right", "top"))) | ||
draw(tech_legend) | ||
upViewport() | ||
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pushViewport(viewport(x = 1.35, y = 1, just = c("right", "top"))) | ||
draw(line_legend) | ||
upViewport() | ||
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dev.off() | ||
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