par(mar = c(1, 1, 1, 1))
circos.par("default.track.height" = 0.1)
circos.initializeWithIdeogram(plotType = NULL)
# data frame with single value column
bed = generateRandomBed(nr = 100)
circos.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
})
circos.genomicTrackPlotRegion(bed, stack = TRUE, panel.fun = function(region, value, ...) {
circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
i = getI(...)
cell.xlim = get.cell.meta.data("cell.xlim")
circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
})
bed1 = generateRandomBed(nr = 100)
bed2 = generateRandomBed(nr = 100)
bed_list = list(bed1, bed2)
# data frame list
circos.genomicTrackPlotRegion(bed_list, panel.fun = function(region, value, ...) {
cex = (value[[1]] - min(value[[1]]))/(max(value[[1]]) - min(value[[1]]))
i = getI(...)
circos.genomicPoints(region, value, cex = cex, pch = 16, col = i, ...)
})
circos.genomicTrackPlotRegion(bed_list, stack = TRUE, panel.fun = function(region, value, ...) {
cex = (value[[1]] - min(value[[1]]))/(max(value[[1]]) - min(value[[1]]))
i = getI(...)
circos.genomicPoints(region, value, cex = cex, pch = 16, col = i, ...)
cell.xlim = get.cell.meta.data("cell.xlim")
circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
})
bed = generateRandomBed(nr = 100, nc = 4)
circos.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
cex = (value[[1]] - min(value[[1]]))/(max(value[[1]]) - min(value[[1]]))
circos.genomicPoints(region, value, cex = 0.5, pch = 16, col = 1:4, ...)
})
circos.genomicTrackPlotRegion(bed, stack = TRUE, panel.fun = function(region, value, ...) {
cex = (value[[1]] - min(value[[1]]))/(max(value[[1]]) - min(value[[1]]))
i = getI(...)
circos.genomicPoints(region, value, cex = cex, pch = 16, col = i, ...)
cell.xlim = get.cell.meta.data("cell.xlim")
circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
})
circos.clear()
##############################################################
### test numeric column
circos.par("default.track.height" = 0.1)
circos.initializeWithIdeogram(plotType = NULL)
bed = generateRandomBed(nr = 10)
circos.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
})
bed = generateRandomBed(nr = 100)
bed = cbind(bed[1:3], rep(1, nrow(bed)), bed[4])
circos.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
})
circos.genomicTrackPlotRegion(bed, numeric.column = 5, panel.fun = function(region, value, ...) {
circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
})
circos.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
circos.genomicPoints(region, value, numeric.column = 1, pch = 16, cex = 0.5, ...)
})
circos.clear()
#####################################################################
### test error situation
circos.par("default.track.height" = 0.1)
circos.initializeWithIdeogram(plotType = NULL)
bed = generateRandomBed(nr = 100, nc = 0)
circos.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
})
bed = cbind(bed, rep("text", nrow(bed)))
circos.genomicTrackPlotRegion(bed, numeric.column = 4, panel.fun = function(region, value, ...) {
circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
})
bed1 = generateRandomBed(nr = 100, nc = 1)
bed2 = generateRandomBed(nr = 100, nc = 1)
bed_list = list(bed1, bed2)
circos.genomicTrackPlotRegion(bed_list, panel.fun = function(region, value, ...) {
circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
})
circos.clear()
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