Add lines for genomic data visualization

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

Usage

ccGenomicLines(
  region = NULL,
  value = NULL,
  numeric.column = NULL,
  posTransform = NULL,
  col = ifelse(area, "grey", "black"),
  lwd = par("lwd"),
  lty = par("lty"),
  type = "l",
  area = FALSE,
  area.baseline = NULL,
  border = "black",
  baseline = "bottom",
  pt.col = par("col"),
  cex = par("cex"),
  pch = par("pch"),
  ...
)

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.

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 explaination.

col

col of lines/areas. If there are more than one numeric column, the length of col can be either one or number of numeric columns. If there is only one numeric column and type is either segment or h, the length of col can be either one or number of rows of region. pass to circos.lines

lwd

Settings are similar as col. Pass to circos.lines.

lty

Settings are similar as col. Pass to circos.lines.

type

There is an additional option segment which plot segment lines from start position to end position. Settings are similar as col. Pass to circos.lines.

area

Settings are similar as col. Pass to circos.lines.

area.baseline

Deprecated, use baseline instead.

border

Settings are similar as col. Pass to circos.lines.

baseline

Settings are similar as col. Pass to circos.lines.

pt.col

Settings are similar as col. Pass to circos.lines.

cex

Settings are similar as col. Pass to circos.lines.

pch

Settings are similar as col. Pass to circos.lines.

...

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) +
ccGenomicLines(numeric.column = 2)
t1 <- t1 + cells1
show(cc + t1)
#> Note: 1 point is out of plotting region in sector 'chr4', track '1'.