circos.genomicPoints: Add points to a plotting region, specifically for genomic...

In eilslabs/circlize: Circular Visualization

Description

Add points to a plotting region, specifically for genomic graphics

Usage

circos.genomicPoints(region, value, numeric.column = NULL,
    sector.index = get.cell.meta.data("sector.index"),
    track.index = get.cell.meta.data("track.index"), posTransform = NULL,
    pch = par("pch"), col = par("col"), cex = par("cex"), bg = par("bg"), ...)

Arguments

region	A data frame contains 2 columns which correspond to start positions and end positions
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.points
track.index	Pass to circos.points
posTransform	Self-defined function to transform genomic positions, see posTransform.default for explanation
col	color of points. If there is only one numeric column, the length of col can be either one or number of rows of region. If there are more than one numeric column, the length of col can be either one or number of numeric columns. Pass to circos.points
pch	Type of points. Settings are similar as col. Pass to circos.points
cex	Size of points. Settings are similar as col. Pass to circos.points
bg	background colors for points.
...	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: 

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

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()


## End(Not run)

eilslabs/circlize documentation built on May 16, 2019, 1:23 a.m.