circos.genomicRainfall: Genomic rainfall plot

Description Usage Arguments Details References Examples

View source: R/genomic.R

Description

Genomic rainfall plot

Usage

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circos.genomicRainfall(data, mode = "min", ylim = NULL, col = "black",
    pch = par("pch"), cex = par("cex"), normalize_to_width = FALSE, ...)

Arguments

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 rainfallTransform

ylim

ylim for rainfall plot track. If normalize_to_width is FALSE, the value should correspond to log10(dist+1), and if normalize_to_width is TRUE, the value should correspond to log2(rel_dist).

col

Color of points. It should be length of one. If data is a list, the length of col can also be the length of the list.

pch

Style of points

cex

Size of points

normalize_to_width

If it is TRUE, the value is the relative distance divided by the width of the region.

...

Pass to circos.trackPlotRegion

Details

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.

References

Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics.

Examples

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## Not run: 
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()


## End(Not run)

jokergoo/circlize documentation built on Aug. 11, 2019, 11:01 a.m.