Overlayed Circular multiple barcharts in R

问题

The following is my data:

chr <- rep (1:4, each = 200) 

position <- c(1:200, 1:200, 1:200, 1:200)

v1bar <- rnorm(800, 10, 2)

v2bar <- rnorm(800, 10, 2)

v3bar <- rnorm(800, 10, 2)

mydata <- data.frame (chr, position, v1bar, v2bar, v3bar)

I want to create multiple circular bar charts with the x value = pos and y value = v1bar, v2bar, v3bar (all three will be in successive circles). Each circle is divided to chr. Thus each circle has "pie slice". I am not sure what such graph is known as and would it be possible to develop one. The following just rough sketch to illustrate my idea.

Edits: My assuption is someway similar to the following circos figure.

http://circos.ca/tutorials/images/zoom/8.8

EDITS:

In response to the following answer to David, this what I have imagined - chr not seperate circe but classifying as different slice (such as in circos figure)

回答1:

Since you are presenting chromosomes in a circular way, try the tools provided by the ecolitk package provided by Bioconductor, which includes tools for plotting various kinds of shapes on circular chromosomes.

ETA: Here is an example of its use to create a circular bar plot, though it only scratches the surface of the things you can do with it.

library(ecolitk)

plot.new()
plot.window(c(-5, 5), c(-5, 5))

plot.chrom = function(data, chromlength, radius=1,
                        width=chromlength/length(data), ...) {
    linesCircle(radius, ...)
    starts = seq(1, chromlength - width, width)

    scale = .5 / max(abs(data))
    for (i in 1:length(starts)) {
        polygonChrom(starts[i], starts[i]+width, chromlength, radius,
                data[i] * scale + radius, ...)
    }
}

plot.chrom(rnorm(100, 10, 1), 10000, radius=1)
plot.chrom(rnorm(100, 10, 2), 10000, radius=2, col="blue")
plot.chrom(rnorm(100, 10, 5), 10000, radius=3, col="red")
plot.chrom(rnorm(100, 10, 10), 10000, radius=4, col="green")

legend("topright", legend=c("chr1", "chr2", "chr3", "chr4"),
       col=c("black", "blue", "red", "green"), lty=1)

ETA: Ah, now I understand what you meant about division of plots. In that case, this code should be what you're looking for. It uses the data you present (with one slight modification- I had to give the chromosome column a name so I could use ddply with it) and allows you to specify the spacing between chromosomes. While I haven't tested it in depth, varying things like the individual chromosome lengths and the mean and variance of the simulated data should work as you expect.

plot.multi.chrom = function(data, colors, spacing=50) {
    plot.new()
    plot.window(c(-5, 5), c(-5, 5))

    lengths = ddply(data, .(chr), function(x) max(x$position))
    nchrom = NROW(lengths)
    offsets = cumsum(c(0, lengths[, 2])) + cumsum(c(0, rep(spacing, nchrom)))
    tot.length = offsets[length(offsets)] + spacing

    scales = .75 / apply(abs(data[, 3:NCOL(data)]), 2, max)

    for (i in 1:NROW(data)) {
        for (j in 3:NCOL(data)) {
            start = offsets[data[i, 1]] + data[i, 2]
            polygonChrom(start, start + 1, tot.length,
                         j - 2, data[i, j] * scales[j - 2] + j - 2,
                         col=colors[j - 2])
        }
    }
}

chr <- rep (1:4, each = 200) 
position <- c(1:200, 1:200, 1:200, 1:200)
v1bar <- rnorm(800, 10, 2)
v2bar <- rnorm(800, 10, 2)
v3bar <- rnorm(800, 10, 2)
mydata <- data.frame(chr=chr, position, v1bar, v2bar, v3bar)

 require(plyr) 

plot.multi.chrom(mydata, colors=c("red", "black", "green"), spacing=50)

legend("topright", legend=c("V1", "V2", "V3"),
       col=c("red", "black", "green"), lty=1)

回答2:

OmicCircos at R/Bioconductor has ability to draw overlayed circular multiple bar charts. OmicCircos's circos command takes argument, named cir where you can specify custom genome segments or chromosomes. For bar chart, it has argument type where you can specify one of bar plot, box plot, histogram, etc.

Check Vignette R script - code chunk number 14: OmicCircos4vignette1 for more.

来源：https://stackoverflow.com/questions/9417711/overlayed-circular-multiple-barcharts-in-r

标签

graph

bar-chart