Description Usage Arguments Details References Examples
Draw rectangle-like grid, specifically for genomic graphics
1 2 3 4 5 | circos.genomicRect(region, value = NULL,
ytop = NULL, ybottom = NULL, ytop.column = NULL, ybottom.column = NULL,
sector.index = get.cell.meta.data("sector.index"),
track.index = get.cell.meta.data("track.index"), posTransform = NULL,
col = NA, border = "black", lty = par("lty"), ...)
|
region |
A data frame contains 2 column which correspond to start position and end position |
value |
A data frame contains values and other information |
ytop |
A vector or a single value indicating top position of rectangles |
ybottom |
A vector or a single value indicating bottom position of rectangles |
ytop.column |
If |
ybottom.column |
If |
sector.index |
Pass to |
track.index |
Pass to |
posTransform |
Self-defined function to transform genomic positions, see |
col |
The length of |
border |
Settings are similar as |
lty |
Settings are similar as |
... |
Mysterious parameters |
The function is a low-level graphical function and usually is put in panel.fun
when using circos.genomicTrackPlotRegion
.
Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics.
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 | ## Not run:
############################
### rect matrix
circos.par("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))
circos.initializeWithIdeogram(plotType = NULL)
bed = generateRandomBed(nr = 100, nc = 4)
circos.genomicTrackPlotRegion(bed, stack = TRUE, panel.fun = function(region, value, ...) {
circos.genomicRect(region, value, col = sample(1:10, nrow(region), replace = TRUE),
border = NA, ...)
i = getI(...)
cell.xlim = get.cell.meta.data("cell.xlim")
#circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
}, bg.border = NA)
circos.genomicPosTransformLines(bed, posTransform = posTransform.default,
horizontalLine = "top")
circos.genomicTrackPlotRegion(bed, stack = TRUE, panel.fun = function(region, value, ...) {
circos.genomicRect(region, value, col = sample(1:10, nrow(region), replace = TRUE),
border = NA, posTransform = posTransform.default, ...)
i = getI(...)
cell.xlim = get.cell.meta.data("cell.xlim")
#circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
}, bg.border = NA)
circos.genomicPosTransformLines(bed, posTransform = posTransform.default,
direction = "outside", horizontalLine = "bottom")
circos.genomicTrackPlotRegion(bed, stack = TRUE, panel.fun = function(region, value, ...) {
circos.genomicRect(region, value, col = sample(1:10, nrow(region), replace = TRUE),
border = NA, ...)
i = getI(...)
cell.xlim = get.cell.meta.data("cell.xlim")
#circos.lines(cell.xlim, c(i, i), lty = 2, col = "#00000040")
}, bg.border = NA)
circos.clear()
##########################
### rect from bed list
circos.par("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))
circos.initializeWithIdeogram(plotType = NULL)
bed1 = generateRandomBed(nr = 100)
bed2 = generateRandomBed(nr = 100)
bed_list = list(bed1, bed2)
f = colorRamp2(breaks = c(-1, 0, 1), colors = c("green", "black", "red"))
circos.genomicTrackPlotRegion(bed_list, stack = TRUE,
panel.fun = function(region, value, ...) {
circos.genomicRect(region, value, col = f(value[[1]]),
border = NA, ...)
i = getI(...)
cell.xlim = get.cell.meta.data("cell.xlim")
circos.lines(cell.xlim, c(i, i), lty = 2, col = "#000000")
})
circos.genomicTrackPlotRegion(bed_list, ylim = c(0, 3),
panel.fun = function(region, value, ...) {
i = getI(...)
circos.genomicRect(region, value, ytop = i+0.4, ybottom = i-0.4, col = f(value[[1]]),
border = NA, ...)
cell.xlim = get.cell.meta.data("cell.xlim")
circos.lines(cell.xlim, c(i, i), lty = 2, col = "#000000")
})
circos.genomicTrackPlotRegion(bed1, panel.fun = function(region, value, ...) {
circos.genomicRect(region, value, col = "red", border = NA, ...)
})
circos.genomicTrackPlotRegion(bed_list, panel.fun = function(region, value, ...) {
i = getI(...)
circos.genomicRect(region, value, col = i, border = NA, ...)
})
circos.clear()
## End(Not run)
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