circlizePlus (version 0.9.0)

ccGenomicRect: 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"),
  ...
)

Value

Object ccGenomicCellGeom

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.

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)