Genomic rainfall plot
Genomic rainfall plot
circos.genomicRainfall(
data,
mode = "min",
ylim = NULL,
col = "black",
pch = par("pch"),
cex = par("cex"),
normalize_to_width = FALSE,
...)data |
A bed-file-like data frame or a list of data frames. |
mode |
How to calculate the distance of two neighbouring regions, pass to |
ylim |
ylim for rainfall plot track. If |
col |
Color of points. It should be length of one. If |
pch |
Style of points. |
cex |
Size of points. |
normalize_to_width |
If it is |
... |
Pass to |
This is high-level graphical function, which mean, it will create a new track.
Rainfall plot can be used to visualize distribution of regions. On the plot, y-axis corresponds to the distance to neighbour regions (log-based). So if there is a drop-down on the plot, it means there is a cluster of regions at that area.
On the plot, y-axis are log10-transformed.
load(system.file(package = "circlize", "extdata", "DMR.RData"))
# 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()Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.