R: Genomic rainfall plot

circos.genomicRainfall {circlize} | R Documentation

## Genomic rainfall plot

### Description

Genomic rainfall plot

### Usage

    circos.genomicRainfall(data, mode = "min", ylim = c(0, 9), col = "black",
        pch = par("pch"), cex = par("cex"), ...)

### Arguments

`data` | A bed-file-like data frame or a list of data frames
`mode` | how to calculate the distance of two neighbouring regions, pass to `rainfallTransform`
`ylim` | ylim for rainfall plot track. It's value should be log10(inter-distance+1)
`col` | Color of points. It should be length of one. If `data` is a list, the length of `col` can also be the length of the list.
`pch` | Style of points
`cex` | Size of points
`...` | Pass to `circos.trackPlotRegion`

### Details

This is high-level graphical function, which mean, it will create a new track.

Rainfall plot can be used to visualize distribution of regions. On the plot, y-axis corresponds to the distance to neighbour regions (log-based). So if there is a drop-down on the plot, it means there is a cluster of regions at that area.

On the plot, y-axis are log10-transformed.

### References

Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics.

### Examples

    ## Not run:
    load(system.file(package = "circlize", "extdata", "DMR.RData"))

    # rainfall
    circos.initializeWithIdeogram(plotType = c("axis", "labels"))

    bed_list = list(DMR_hyper, DMR_hypo)
    circos.genomicRainfall(bed_list, pch = 16, cex = 0.4, col = c("#FF000080", "#0000FF80"))

    circos.genomicDensity(bed_list[[1]], col = c("#FF000080"), track.height = 0.1)
    circos.genomicDensity(bed_list[[2]], col = c("#0000FF80"), track.height = 0.1)

    circos.clear()

    ## End(Not run)

[Package circlize version 0.4.1 Index]