Define a heatmap track for genomic graph — ccGenomicHeatmap • circlizePlus

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")
#> Warning: `convert_length()` only works when aspect of the coordinate is 1.
cc + t1

circos.clear()