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

In eilslabs/circlize: Circular Visualization

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"), lwd = par("lwd"), ...)

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
lwd	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.

References

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

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()


## End(Not run)

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