circos.genomicPosTransformLines: Add genomic position transformation lines between tracks

In eilslabs/circlize: Circular Visualization

Description

Add genomic position transformation lines between tracks

Usage

circos.genomicPosTransformLines(data, track.height = 0.1, posTransform = NULL,
    horizontalLine = c("none", "top", "bottom", "both"), track.margin = c(0, 0),
    direction = c("inside", "outside"), col = "black", lwd = par("lwd"),
    lty = par("lty"), ...)

Arguments

data	A data frame containing genomic data
track.height	Height of the track
posTransform	Genomic position transformation function, see posTransform.default for an example.
horizontalLine	Whether to draw horizontal lines which indicate region width
track.margin	Margin of tracks
direction	Type of the transformation. inside means position transformed track are located inside and outside means position transformed track are located outside.
col	Color of lines, can be length of one or nrow of data
lwd	Width of lines
lty	Style of lines
...	pass to circos.trackPlotRegion

Details

There is one representative situation when such position transformation needs to be applied. For example, there are two sets of regions in a chromosome in which regions in one set regions are quite densely to each other and regions in other set are far from others. Heatmap or text is going to be drawn on the next track. If there is no position transformation, heatmap or text for those dense regions would be overlapped and hard to identify, also ugly to visualize. Thus, a way to transform original positions to new positions would help for the visualization.

References

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

Examples

## Not run: 

par(mfrow = c(2, 1))
### rect matrix
circos.par(cell.padding = c(0, 0, 0, 0))
circos.initializeWithIdeogram()

bed = generateRandomBed(nr = 100, nc = 4)

circos.genomicPosTransformLines(bed, posTransform = posTransform.default,
    horizontalLine = "top", track.height = 0.1)

f = colorRamp2(breaks = c(-1, 0, 1), colors = c("green", "black", "red"))
circos.genomicTrackPlotRegion(bed, stack = TRUE, panel.fun = function(region, value, ...) {
    circos.genomicRect(region, value, col = f(value[[1]]), 
        border = f(value[[1]]), posTransform = posTransform.default, ...)
}, bg.border = NA)

circos.clear()


circos.par(cell.padding = c(0, 0, 0, 0))
circos.initializeWithIdeogram(plotType = NULL)

bed = generateRandomBed(nr = 20, nc = 4)

circos.genomicTrackPlotRegion(bed, ylim = c(0, 1), panel.fun = function(region, value, ...) {
    circos.genomicText(region, value, y = 0, adj = c(1, 0.5),
        labels = "gene", facing = "reverse.clockwise",
        posTransform = posTransform.default)
}, bg.border = NA)

circos.genomicPosTransformLines(bed, posTransform = posTransform.default,
    horizontalLine = "bottom", direction = "outside", track.height = 0.1)

cytoband = read.cytoband()$df
circos.genomicTrackPlotRegion(cytoband, stack = TRUE, panel.fun = function(region, value, ...) {
    circos.genomicRect(region, value, col = cytoband.col(value$V5), border = NA, ...)
}, track.height = 0.05)

circos.clear()

## End(Not run)

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