ccGenomicPoints: Add points for genomic data visualization

In circlizePlus: Using 'ggplot2' Feature to Write Readable R Code for Circular Visualization

Add points for genomic data visualization

Description

Object ccGenomicCellGeom will call the function circlize::circos.genomicPoints while drawing.

Usage

ccGenomicPoints(
  region = NULL,
  value = NULL,
  numeric.column = NULL,
  posTransform = NULL,
  pch = par("pch"),
  col = par("col"),
  cex = par("cex"),
  bg = par("bg"),
  ...
)

Arguments

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 value data frame should be taken as y-value. If it is not defined, the whole numeric columns in value will be taken.
posTransform	Self-defined function to transform genomic positions, see posTransform.default for explanation
pch	Type of points. Settings are similar as col. Pass to circos.points.
col	Color of points. If there is only one numeric column, the length of col can be either one or number of rows of region. If there are more than one numeric column, the length of col can be either one or number of numeric columns. Pass to circos.points.
cex	Size of points. Settings are similar as col. Pass to circos.points.
bg	Background colors for points.
...	Mysterious parameters.

Value

Object ccGenomicCellGeom

Examples

library(circlizePlus)
data <- generateRandomBed(nr = 30, nc = 2)
all_chr <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8",
"chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16",
"chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY")
cc <- ccPlot(initMode = "initializeWithIdeogram", plotType = NULL)
t1 <- ccGenomicTrack(data = data, numeric.column = 4)
cells1 <- ccCells(sector.indexes = all_chr) +
ccGenomicPoints(region = \(region, value){
  region
}, value = \(region, value){
  value
}, numeric.column = 2)
t1 <- t1 + cells1
show(cc + t1)

circlizePlus documentation built on June 8, 2025, 10:42 a.m.