circlize (version 0.4.1)

circos.genomicPosTransformLines: Add genomic position transformation lines between tracks

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()
# }
# NOT RUN {
# }