ccGenomicHeatmap: Define a heatmap track for genomic graph

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

Define a heatmap track for genomic graph

Description

Object ccGenomicTrack will call the function circlize::circos.genomicHeatmap while drawing.

Usage

ccGenomicHeatmap(
  bed,
  col,
  na_col = "grey",
  numeric.column = NULL,
  border = NA,
  border_lwd = par("lwd"),
  border_lty = par("lty"),
  connection_height = mm_h(5),
  line_col = par("col"),
  line_lwd = par("lwd"),
  line_lty = par("lty"),
  heatmap_height = 0.15,
  side = c("inside", "outside"),
  track.margin = circos.par("track.margin")
)

Arguments

bed	A data frame in bed format, the matrix should be stored from the fourth column.
col	Colors for the heatmaps. The value can be a matrix or a color mapping function generated by colorRamp2.
na_col	Color for NA values.
numeric.column	Column index for the numeric columns. The values can be integer index or character index. By default it takes all numeric columns from the fourth column.
border	Border of the heatmap grids.
border_lwd	Line width for borders of heatmap grids.
border_lty	Line style for borders of heatmap grids.
connection_height	Height of the connection lines. If it is set to NULL, no connection will be drawn. Use mm_h/cm_h/inches_h to set a height in absolute unit.
line_col	Color of the connection lines. The value can be a vector.
line_lwd	Line width of the connection lines.
line_lty	Line style of the connection lines.
heatmap_height	Height of the heatmap track
side	Side of the heatmaps. Is the heatmap facing inside or outside?
track.margin	Bottom and top margins.

Value

Object ccGenomicTrack

Examples

library(circlizePlus)
cc = ccPlot(initMode = "initializeWithIdeogram")
bed = generateRandomBed(nr = 100, nc = 4)
col_fun = colorRamp2(c(-1, 0, 1), c("green", "black", "red"))
t1 = ccGenomicHeatmap(bed, col = col_fun, side = "inside", border = "white")
cc + t1
circos.clear()

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