Last data update: 2014.03.03
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R: Calculate and add genomic density track
circos.genomicDensity | R Documentation |
Calculate and add genomic density track
Description
Calculate and add genomic density track
Usage
circos.genomicDensity(data, ylim.force = FALSE, window.size = NULL, overlap = TRUE,
col = ifelse(area, "grey", "black"), lwd = par("lwd"), lty = par("lty"), type = "l",
area = TRUE, area.baseline = NULL, baseline = 0, border = NA, ...)
Arguments
data |
A bed-file-like data frame or a list of data frames
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ylim.force |
Whether to force upper bound of ylim to be 1.
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window.size |
Pass to genomicDensity
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overlap |
Pass to genomicDensity
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col |
Colors. It should be length of one. If data is a list of data frames, the length of col
can also be the length of the list.
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lwd |
Width of lines
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lty |
Style of lines
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type |
Type of lines, see circos.lines
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area |
See circos.lines
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area.baseline |
Deprecated, use baseline instead.
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baseline |
See circos.lines
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border |
See circos.lines
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... |
Pass to circos.trackPlotRegion
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Details
This function is a high-level graphical function, and it will create a new track.
References
Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics.
Examples
## Not run:
library(circlize)
par(mar = c(1, 1, 1, 1))
load(paste(system.file(package = "circlize"), "/extdata/DMR.RData", sep=""))
# rainfall
circos.initializeWithIdeogram(plotType = c("axis", "labels"))
bed_list = list(DMR_hyper, DMR_hypo)
circos.genomicRainfall(bed_list, pch = 16, cex = 0.4, col = c("#FF000080", "#0000FF80"))
circos.genomicDensity(bed_list[[1]], col = c("#FF000080"), track.height = 0.1)
circos.genomicDensity(bed_list[[2]], col = c("#0000FF80"), track.height = 0.1)
circos.clear()
## End(Not run)
Results
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