How to plot overlapping ranges with ggplot2

Question

I am trying to get my head around `ggplot2`. In particular, I am trying to find out if there is a better (more elegant, simpler) way of creating the plot found in the `Bioconductor` `IRanges` package vignette (found here, figure on page 12, code on page 11). In the vignette, the plot is produced with the following code: ``` plotRanges <- function(x, xlim = x, main = deparse(substitute(x)), + col = "black", sep = 0.5, ...) +{ + height <- 1 + if (is(xlim, "Ranges")) + xlim <- c(min(start(xlim)), max(end(xlim))) + bins <- disjointBins(IRanges(start(x), end(x) + 1)) + plot.new() + plot.window(xlim, c(0, max(bins)*(height + sep))) + ybottom <- bins * (sep + height) - height + rect(start(x)-0.5, ybottom, end(x)+0.5, ybottom + height, col = col, ...) + title(main) + axis(1) +} ir <- IRanges(c(1, 8, 14, 15, 19, 34, 40), + width = c(12, 6, 6, 15, 6, 2, 7)) plotRanges(ir) ``` The fact that the stacked bars are created by drawing rectangles and one has to calculate the corner points, height and…

Accepted Answer

Here's a way to produce a similar plot using `ggplot2`. I use the example data of `IRanges`.

```
library(IRanges)

# example data
ir <- IRanges(c(1, 8, 14, 15, 19, 34, 40),
              width = c(12, 6, 6, 15, 6, 2, 7))
# IRanges of length 7
#     start end width
# [1]     1  12    12
# [2]     8  13     6
# [3]    14  19     6
# [4]    15  29    15
# [5]    19  24     6
# [6]    34  35     2
# [7]    40  46     7

bins <- disjointBins(IRanges(start(ir), end(ir) + 1))
# [1] 1 2 1 2 3 1 1

dat <- cbind(as.data.frame(ir), bin = bins)

library(ggplot2)
ggplot(dat) + 
         geom_rect(aes(xmin = start, xmax = end,
                       ymin = bin, ymax = bin + 0.9)) +
  theme_bw()
```

How to plot overlapping ranges with ggplot2

Solution

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