ccGenomicRect: Draw rectangle for genomic data visualization

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

Draw rectangle for genomic data visualization

Description

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

Usage

ccGenomicRect(
  region = NULL,
  value = NULL,
  ytop = NULL,
  ybottom = NULL,
  ytop.column = NULL,
  ybottom.column = NULL,
  posTransform = NULL,
  col = NA,
  border = "black",
  lty = par("lty"),
  ...
)

Arguments

region	A data frame contains 2 column which correspond to start positions and end positions.
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 ytop is in value, the index of the column.
ybottom.column	If ybottom is in value, the index of the column.
posTransform	Self-defined function to transform genomic positions, see posTransform.default for explaination.
col	The length of col can be either one or number of rows of region. Pass to circos.rect.
border	Settings are similar as col. Pass to circos.rect.
lty	Settings are similar as col. Pass to circos.rect.
...	Mysterious parameters.

Value

Object ccGenomicCellGeom

Examples

library(circlizePlus)
par1 <- ccPar("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))
cc <- ccPlot(initMode = "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"))
track1 <- ccGenomicTrack(data = bed_list, stack = TRUE)
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")
rect1 <- ccGenomicRect(col = 1, border = NA)
cells1 <- ccCells(sector.indexes = all_chr) + rect1
cc + par1 + (track1 + cells1)

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