Create circlize.R

circlize.R

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+
+devtools::install_github("jokergoo/circlize") 
+library(circlize)
+
+set.seed(123)
+df = generateRandomBed(30)[ , 1:3]
+df[, 3] = df[, 2]
+df$gene = paste0("gene_", 1:nrow(df))
+df$pathway = paste0("pathway_", sample(10, nrow(df), replace = TRUE))
+head(df)
+
+cytoband = read.cytoband()$df
+cytoband = rbind(cytoband,
+                 data.frame(V1 = "pathway", V2 = 1,  V3 = 2e8, V4 = "", V5 = "")
+)
+tail(cytoband)
+
+cytoband = read.cytoband()$df
+cytoband = rbind(cytoband,
+                 data.frame(V1 = "pathway", V2 = 1,  V3 = 2e8, V4 = "", V5 = "")
+)
+tail(cytoband)
+
+foo = round(seq(1, 2e8, length = 11))
+pathway_mid = structure(as.integer((foo[1:10] + foo[2:11])/2), 
+                        names = paste0("pathway_", 1:10))
+
+df$pathway_chr = "pathway"
+df$pathway_start = pathway_mid[ df$pathway ]
+df$pathway_end = pathway_mid[ df$pathway ]
+head(df)
+
+circos.initializeWithIdeogram(cytoband)
+circos.genomicLink(df[, 1:3], df[, 6:8])
+
+
+## That is basically the idea. Next I customize the plot to make it look nicer, e.g., to adjust font size, set colors, add labels, …
+
+circos.par(gap.after = c(rep(1, 23), 5, 5))
+circos.genomicInitialize(cytoband, plotType = NULL)
+
+# the labels track
+label_df = rbind(df[, 1:4], setNames(df[, c(6:8, 5)], colnames(df)[1:4]))
+label_df = unique(label_df)
+circos.genomicLabels(label_df, labels.column = 4, side = "outside", cex = 0.6)
+
+# the chromosome names track
+circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
+  circos.text(CELL_META$xcenter, CELL_META$ylim[1], CELL_META$sector.index,
+              niceFacing = TRUE, adj = c(0.5, 0), cex = 0.8)
+}, track.height = strheight("fj", cex = 0.8)*1.2, bg.border = NA, cell.padding = c(0, 0, 0, 0))
+
+# ideogram track
+circos.genomicIdeogram(cytoband)
+
+# add points to the cell "pathway"
+tb = table(df$pathway)
+pathway_col = structure(1:10, names = paste0("pathway_", 1:10))
+set.current.cell(sector.index = "pathway", track.index = get.current.track.index())
+circos.points(x = pathway_mid[names(tb)], y = CELL_META$ycenter, pch = 16,
+              cex = tb/5, col = pathway_col[names(tb)])
+
+# genomic links
+circos.genomicLink(df[, 1:3], df[, 6:8], col = pathway_col[df[, 5]])