R: Add lines to a plotting region, specifically for genomic...

circos.genomicLines {circlize} | R Documentation

## Add lines to a plotting region, specifically for genomic graphics

### Description

Add lines to a plotting region, specifically for genomic graphics

### Usage

    circos.genomicLines(region, value, numeric.column = NULL,
        sector.index = get.cell.meta.data("sector.index"),
        track.index = get.cell.meta.data("track.index"), posTransform = NULL,
        col = ifelse(area, "grey", "black"), lwd = par("lwd"),
        lty = par("lty"), type = "l",
        area = FALSE, area.baseline = NULL, border = "black", baseline = "bottom",
        pt.col = par("col"), cex = par("cex"), pch = par("pch"), ...)

### Arguments

`region` | A data frame contains 2 column which correspond to start position and end position
`value` | A data frame contains values and other information
`numeric.column` | Which column in `value` data frame should be taken as y-value. If it is not defined, the whole numeric columns in `value` will be taken.
`sector.index` | Pass to `circos.lines`
`track.index` | Pass to `circos.lines`
`posTransform` | Self-defined function to transform genomic positions, see `posTransform.default` for explaination
`col` | col of lines/areas. If there are more than one numeric column, the length of `col` can be either one or number of numeric columns. If there is only one numeric column and type is either `segment` or `h`, the length of `col` can be either one or number of rows of `region`. pass to `circos.lines`
`lwd` | Settings are similar as `col`. Pass to `circos.lines`
`lty` | Settings are similar as `col`. Pass to `circos.lines`
`type` | There is an additional option `segment` which plot segment lines from start position to end position. Settings are similar as `col`. Pass to `circos.lines`.
`area` | Settings are similar as `col`. Pass to `circos.lines`
`area.baseline` | Deprecated, use `baseline` instead.
`baseline` | Settings are similar as `col`. Pass to `circos.lines`
`border` | Settings are similar as `col`. Pass to `circos.lines`
`pt.col` | Settings are similar as `col`. Pass to `circos.lines`
`cex` | Settings are similar as `col`. Pass to `circos.lines`
`pch` | Settings are similar as `col`. Pass to `circos.lines`
`...` | mysterious parameters

### Details

The function is a low-level graphical function and usually is put in `panel.fun` when using `circos.genomicTrackPlotRegion`.

### References

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

### Examples

    ## Not run:

    ### test bed
    circos.par("track.height" = 0.1)
    circos.initializeWithIdeogram(plotType = NULL)

    bed = generateRandomBed(nr = 100)
    circos.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
        circos.genomicLines(region, value, type = "l", ...)
    })

    bed1 = generateRandomBed(nr = 100)
    bed2 = generateRandomBed(nr = 100)
    bed_list = list(bed1, bed2)

    circos.genomicTrackPlotRegion(bed_list, panel.fun = function(region, value, ...) {
        i = getI(...)
        circos.genomicLines(region, value, col = i, ...)
    })

    circos.genomicTrackPlotRegion(bed_list, stack = TRUE,
        panel.fun = function(region, value, ...) {
        i = getI(...)
        circos.genomicLines(region, value, col = i, ...)
    })

    bed = generateRandomBed(nr = 100, nc = 4)
    circos.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
        circos.genomicLines(region, value, col = 1:4, ...)
    })

    circos.genomicTrackPlotRegion(bed, stack = TRUE, panel.fun = function(region, value, ...) {
        i = getI(...)
        circos.genomicLines(region, value, col = i, ...)
    })

    bed = generateRandomBed(nr = 100)
    circos.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
        circos.genomicLines(region, value, type = "segment", lwd = 2, ...)
    })

    circos.clear()

    ## End(Not run)

[Package circlize version 0.4.5 Index]