intra- and inter-translocations

translocations.R

x = sort(runif(20))

df1 = data.frame(x1 = x[1:20 %% 2 == 0], x2 = x[1:20 %% 2 == 1])
df1 = cbind(gene = "A", df1)

x = sort(runif(10, max = 0.5))

df2 = data.frame(x1 = x[1:10 %% 2 == 0], x2 = x[1:10 %% 2 == 1])
df2 = cbind(gene = "B", df2)



x = sort(runif(30, max = 2))

df3 = data.frame(x1 = x[1:30 %% 2 == 0], x2 = x[1:30 %% 2 == 1])
df3 = cbind(gene = "C", df3)


df = rbind(df1, df2, df3)

link = data.frame(gene1 = sample(c("A", "B", "C"), nrow(df), replace = TRUE),
    x1 = 0,
    gene2 = sample(c("A", "B", "C"), nrow(df), replace = TRUE),
    x2 = 0)
for(i in seq_len(nrow(link))) {
	if(link$gene1[i] == "A") {
		link$x1[i] = runif(1)
	} else if(link$gene1[i] == "B") {
		link$x1[i] = runif(1, max = 0.5)
	} else if(link$gene1[i] == "C") {
		link$x1[i] = runif(1, max = 2)
	}

	if(link$gene2[i] == "A") {
		link$x2[i] = runif(1)
	} else if(link$gene2[i] == "B") {
		link$x2[i] = runif(1, max = 0.5)
	} else if(link$gene2[i] == "C") {
		link$x2[i] = runif(1, max = 2)
	}
}   


circos.par(circle.margin = 0.1, gap.degree = 5)
circos.initialize(c("A", "B", "C"), xlim = cbind(c(0, 0, 0), c(1, 0.5, 2)))

circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
	tb = df[df[, 1] == CELL_META$sector.index, ]
	circos.lines(CELL_META$xlim, c(0.5, 0.5), col = "grey")
	circos.rect(tb[, 2], 0.1, tb[, 3], 0.9, col = 1+CELL_META$sector.numeric.index, border = "grey")
}, track.height = mm_h(4), bg.border = NA, bg.col = "#EEEEEE")

for(i in seq_len(nrow(link))) {
	if(link$gene1[i] == link$gene2[i]) {
		circos.link(link$gene1[i], link$x1[i], link$gene2[i], link$x2[i], h = -0.1, rou = 1, col = 5, w = 0.1)
	} else {
		circos.link(link$gene1[i], link$x1[i], link$gene2[i], link$x2[i], col = 6)
	}
}
circos.clear()