circlize (version 0.4.10)

circos.genomicRect: Draw rectangle-like grid, specifically for genomic graphics

Description

Draw rectangle-like grid, specifically for genomic graphics

Usage

circos.genomicRect(
    region,
    value = NULL,
    ytop = NULL,
    ybottom = NULL,
    ytop.column = NULL,
    ybottom.column = NULL,
    sector.index = get.cell.meta.data("sector.index"),
    track.index = get.cell.meta.data("track.index"),
    posTransform = NULL,
    col = NA,
    border = "black",
    lty = par("lty"),
    ...)

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

ytop

A vector or a single value indicating top position of rectangles

ybottom

A vector or a single value indicating bottom position of rectangles

ytop.column

If ytop is in value, the index of the column

ybottom.column

If ybottom is in value, the index of the column

sector.index

Pass to circos.rect

track.index

Pass to circos.rect

posTransform

Self-defined function to transform genomic positions, see posTransform.default for explaination

col

The length of col can be either one or number of rows of region. Pass to circos.rect

border

Settings are similar as col. Pass to circos.rect

lty

Settings are similar as col. Pass to circos.rect

...

Mysterious parameters

Details

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

Examples

# NOT RUN {
############################
### rect matrix
circos.par("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))
circos.initializeWithIdeogram(plotType = NULL)

bed = generateRandomBed(nr = 100, nc = 4)
circos.genomicTrackPlotRegion(bed, stack = TRUE, panel.fun = function(region, value, ...) {
    circos.genomicRect(region, value, col = sample(1:10, nrow(region), replace = TRUE), 
        border = NA, ...)
    i = getI(...)
    cell.xlim = get.cell.meta.data("cell.xlim")
    #circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
}, bg.border = NA)

circos.genomicPosTransformLines(bed, posTransform = posTransform.default,
    horizontalLine = "top")

circos.genomicTrackPlotRegion(bed, stack = TRUE, panel.fun = function(region, value, ...) {
    circos.genomicRect(region, value, col = sample(1:10, nrow(region), replace = TRUE), 
        border = NA, posTransform = posTransform.default, ...)
    i = getI(...)
    cell.xlim = get.cell.meta.data("cell.xlim")
    #circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
}, bg.border = NA)

circos.genomicPosTransformLines(bed, posTransform = posTransform.default,
    direction = "outside", horizontalLine = "bottom")

circos.genomicTrackPlotRegion(bed, stack = TRUE, panel.fun = function(region, value, ...) {
    circos.genomicRect(region, value, col = sample(1:10, nrow(region), replace = TRUE), 
        border = NA, ...)
    i = getI(...)
    cell.xlim = get.cell.meta.data("cell.xlim")
    #circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
}, bg.border = NA)

circos.clear()

##########################
### rect from bed list
circos.par("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))
circos.initializeWithIdeogram(plotType = NULL)

bed1 = generateRandomBed(nr = 100)
bed2 = generateRandomBed(nr = 100)
bed_list = list(bed1, bed2)
f = colorRamp2(breaks = c(-1, 0, 1), colors = c("green", "black", "red"))
circos.genomicTrackPlotRegion(bed_list, stack = TRUE,
    panel.fun = function(region, value, ...) {

circos.genomicRect(region, value, col = f(value[[1]]), 
        border = NA, ...)
    i = getI(...)
    cell.xlim = get.cell.meta.data("cell.xlim")
    circos.lines(cell.xlim, c(i, i), lty = 2, col = "#000000")
})

circos.genomicTrackPlotRegion(bed_list, ylim = c(0, 3),
    panel.fun = function(region, value, ...) {
    i = getI(...)
    circos.genomicRect(region, value, ytop = i+0.4, ybottom = i-0.4, col = f(value[[1]]), 
        border = NA, ...)

cell.xlim = get.cell.meta.data("cell.xlim")
    circos.lines(cell.xlim, c(i, i), lty = 2, col = "#000000")
})

circos.genomicTrackPlotRegion(bed1, panel.fun = function(region, value, ...) {
    circos.genomicRect(region, value, col = "red", border = NA, ...)

})

circos.genomicTrackPlotRegion(bed_list, panel.fun = function(region, value, ...) {
    i = getI(...)
    circos.genomicRect(region, value, col = i, border = NA, ...)

})

circos.clear()
# }