circlize (version 0.4.1)

posTransform.text: Genomic position transformation function specifically for text

Description

Genomic position transformation function specifically for text

Usage

posTransform.text(region, y, labels, cex = 1, font = par("font"),
    sector.index = get.cell.meta.data("sector.index"),
    track.index = get.cell.meta.data("track.index"), padding = 0,
    extend = 0, ...)

Arguments

region

Genomic positions at a single chromosome. It is a data frame with two columns which are start position and end position.

y

positions of texts

labels

text labels

cex

text size

font

text font style

sector.index

sector index

track.index

track index

padding

padding of text

extend

extend to allow labels to be put in an region which is wider than the current chromosome. The value should be a proportion value and the length is either one or two.

...

other arguments

Details

This position transformation function is designed specifically for text. Under the transformation, texts will be as close as possible to the original positions.

Examples

# NOT RUN {
op = par(no.readonly = TRUE)

set.seed(123458)

par(mfrow = c(2, 2))

bed = generateRandomBed(nr = 400, fun = function(k) rep("text", k))
bed = bed[-(9:13), ]
##########################################
circos.par("start.degree" = 90, canvas.xlim = c(0, 1), canvas.ylim = c(0, 1), 
    gap.degree = 270, cell.padding = c(0, 0, 0, 0), track.margin = c(0.005, 0.005))
circos.initializeWithIdeogram(plotType = c("axis"), chromosome.index = "chr1")
circos.genomicTrackPlotRegion(bed, ylim = c(0, 1), 
    panel.fun = function(region, value, ...) {
        circos.genomicText(region, value, y = 0, labels.column = 1, 
            facing = "clockwise", adj = c(0, 0.5),
            posTransform = posTransform.text, cex = 0.8, niceFacing = F)
}, track.height = 0.1, bg.border = NA)
i_track = get.cell.meta.data("track.index")

circos.genomicPosTransformLines(bed, 
    posTransform = function(region, value) 
        posTransform.text(region, y = 0, labels = value[[1]], 
            cex = 0.8, track.index = i_track),
    direction = "outside"
)

circos.genomicTrackPlotRegion(bed, ylim = c(0, 1), 
    panel.fun = function(region, value, ...) {
        circos.points( (region[[1]] + region[[2]])/2, rep(0.5, nrow(region)), pch = 16)
}, track.height = 0.02, bg.border = NA)

circos.clear()

text(0, 0.05, "posTransform.text\ndirection = 'outside'", adj = c(0, 0))

############################################
circos.par("start.degree" = 90, canvas.xlim = c(0, 1), canvas.ylim = c(0, 1), 
    gap.degree = 270, cell.padding = c(0, 0, 0, 0), track.margin = c(0.005, 0.005))
circos.initializeWithIdeogram(plotType = c("axis"), chromosome.index = "chr1")
circos.genomicTrackPlotRegion(bed, ylim = c(0, 1), 
    panel.fun = function(region, value, ...) {
        circos.genomicText(region, value, y = 0, labels.column = 1, 
            facing = "clockwise", adj = c(0, 0.5),
            posTransform = posTransform.default, cex = 0.8, niceFacing = F)
}, track.height = 0.1, bg.border = NA)
i_track = get.cell.meta.data("track.index")

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

circos.genomicTrackPlotRegion(bed, ylim = c(0, 1), 
    panel.fun = function(region, value, ...) {
        circos.points( (region[[1]] + region[[2]])/2, rep(0.5, nrow(region)), pch = 16)
}, track.height = 0.02, bg.border = NA)

circos.clear()
text(0, 0.05, "posTransform.default\ndirection = 'outside'", adj = c(0, 0))

##############################################################################
circos.par("start.degree" = 90, canvas.xlim = c(0, 1), canvas.ylim = c(0, 1), 
    gap.degree = 270, cell.padding = c(0, 0, 0, 0), track.margin = c(0.005, 0.005))
circos.initializeWithIdeogram(plotType = c("axis"), chromosome.index = "chr1")
circos.par(cell.padding = c(0, 0, 0, 0))
circos.genomicTrackPlotRegion(bed, ylim = c(0, 1), 
    panel.fun = function(region, value, ...) {
        circos.points( (region[[1]] + region[[2]])/2, rep(0.5, nrow(region)), pch = 16)
}, track.height = 0.02, bg.border = NA)

circos.genomicTrackPlotRegion(bed, ylim = c(0, 1), track.height = 0.1, bg.border = NA)
i_track = get.cell.meta.data("track.index")

circos.genomicTrackPlotRegion(bed, ylim = c(0, 1), 
    panel.fun = function(region, value, ...) {
        circos.genomicText(region, value, y = 1, labels.column = 1, 
            facing = "clockwise", adj = c(1, 0.5),
            posTransform = posTransform.text, cex = 0.8, niceFacing = F)
}, track.height = 0.1, bg.border = NA)

circos.genomicPosTransformLines(bed, 
    posTransform = function(region, value) 
        posTransform.text(region, y = 1, labels = value[[1]], 
            cex = 0.8, track.index = i_track+1),
    direction = "inside", track.index = i_track
)
circos.clear()
text(0, 0.05, "posTransform.text\ndirection = 'inside'", adj = c(0, 0))

##############################################################################
circos.par("start.degree" = 90, canvas.xlim = c(0, 1), canvas.ylim = c(0, 1), 
    gap.degree = 270, cell.padding = c(0, 0, 0, 0), track.margin = c(0.005, 0.005))
circos.initializeWithIdeogram(plotType = c("axis"), chromosome.index = "chr1")
circos.par(cell.padding = c(0, 0, 0, 0))
circos.genomicTrackPlotRegion(bed, ylim = c(0, 1), 
    panel.fun = function(region, value, ...) {
        circos.points( (region[[1]] + region[[2]])/2, rep(0.5, nrow(region)), pch = 16)
}, track.height = 0.02, bg.border = NA)

circos.genomicTrackPlotRegion(bed, ylim = c(0, 1), track.height = 0.1, bg.border = NA)
i_track = get.cell.meta.data("track.index")

circos.genomicTrackPlotRegion(bed, ylim = c(0, 1), 
    panel.fun = function(region, value, ...) {
        circos.genomicText(region, value, y = 1, labels.column = 1, facing = "clockwise", 
            adj = c(1, 0.5), posTransform = posTransform.text, cex = 0.8, 
            niceFacing = F, padding = 0.2)
}, track.height = 0.1, bg.border = NA)


circos.genomicPosTransformLines(bed, 
    posTransform = function(region, value) 
        posTransform.text(region, y = 1, labels = value[[1]], 
            cex = 0.8, track.index = i_track+1, padding = 0.2),
    direction = "inside", track.index = i_track
)
circos.clear()
text(0, 0.05, "posTransform.text\ndirection = 'inside'\npadding = 0.2", adj = c(0, 0))

par(op)

# }
# NOT RUN {
# }