posTransform.text: Genomic position transformation function specifically for...
In eilslabs/circlize: Circular Visualization
Description
Usage
Arguments
Details
Examples
Description
Genomic position transformation function specifically for text
Usage
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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
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## 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)
## End(Not run)
eilslabs/circlize documentation built on May 16, 2019, 1:23 a.m.
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Description Usage Arguments Details Examples
Description
Genomic position transformation function specifically for text
Usage
1 2 3 4 | 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 | ## 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)
## End(Not run)
|
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