circlizePlus (version 0.9.0)

ccGenomicHeatmap: 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")
)

Value

Object ccGenomicTrack

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.

Examples

# \donttest{
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()
# }