Add points to a plotting region, specifically for genomic graphics
Add points to a plotting region, specifically for genomic graphics
circos.genomicPoints(
region,
value,
numeric.column = NULL,
sector.index = get.cell.meta.data("sector.index"),
track.index = get.cell.meta.data("track.index"),
posTransform = NULL,
pch = par("pch"),
col = par("col"),
cex = par("cex"),
bg = par("bg"),
...)region |
A data frame contains 2 columns which correspond to start positions and end positions. |
value |
A data frame contains values and other information. |
numeric.column |
Which column in |
sector.index |
Index of sector. |
track.index |
Index of track. |
posTransform |
Self-defined function to transform genomic positions, see |
col |
Color of points. If there is only one numeric column, the length of |
pch |
Type of points. Settings are similar as |
cex |
Size of points. Settings are similar as |
bg |
Background colors for points. |
... |
Mysterious parameters. |
The function is a low-level graphical function and usually is put in panel.fun when using circos.genomicTrack.
The function behaviours differently from different formats of input, see the examples in the "Examples" Section or go to https://jokergoo.github.io/circlize_book/book/modes-of-input.html for more details.
circos.par("track.height" = 0.1)
circos.initializeWithIdeogram(plotType = NULL)
bed = generateRandomBed(nr = 100)
circos.genomicTrack(bed, panel.fun = function(region, value, ...) {
circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
})
circos.genomicTrack(bed, stack = TRUE, panel.fun = function(region, value, ...) {
circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
i = getI(...)
cell.xlim = get.cell.meta.data("cell.xlim")
circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
})
bed1 = generateRandomBed(nr = 100)
bed2 = generateRandomBed(nr = 100)
bed_list = list(bed1, bed2)
# data frame list
circos.genomicTrack(bed_list, panel.fun = function(region, value, ...) {
cex = (value[[1]] - min(value[[1]]))/(max(value[[1]]) - min(value[[1]]))
i = getI(...)
circos.genomicPoints(region, value, cex = cex, pch = 16, col = i, ...)
})
circos.genomicTrack(bed_list, stack = TRUE,
panel.fun = function(region, value, ...) {
cex = (value[[1]] - min(value[[1]]))/(max(value[[1]]) - min(value[[1]]))
i = getI(...)
circos.genomicPoints(region, value, cex = cex, pch = 16, col = i, ...)
cell.xlim = get.cell.meta.data("cell.xlim")
circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
})
bed = generateRandomBed(nr = 100, nc = 4)
circos.genomicTrack(bed, panel.fun = function(region, value, ...) {
cex = (value[[1]] - min(value[[1]]))/(max(value[[1]]) - min(value[[1]]))
circos.genomicPoints(region, value, cex = 0.5, pch = 16, col = 1:4, ...)
})
circos.genomicTrack(bed, stack = TRUE, panel.fun = function(region, value, ...) {
cex = (value[[1]] - min(value[[1]]))/(max(value[[1]]) - min(value[[1]]))
i = getI(...)
circos.genomicPoints(region, value, cex = cex, pch = 16, col = i, ...)
cell.xlim = get.cell.meta.data("cell.xlim")
circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
})
circos.clear()Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.