plot_chord_diagram Helper function to plot a circlize circos chord diagram

Usage

plot_chord_diagram(
  data.mat,
  color.pal,
  start.degree = 90,
  cell.padding = c(0.02, 0, 0.02, 0),
  circle.margin = 1,
  facing = "clockwise",
  adj = c(0, 0.5),
  cex = 0.8,
  ...,
  gg.output = TRUE
)

Arguments

data.mat: feature 1 (rows) x feature 2 (cols) matrix, with values being interaction counts
color.pal: A named vector of colors. Names correspond to unique feature values, e.g. for cell type features, c("tumor_cell" = "red", "epithelial_cell" = "blue")
start.degree: Passed to circlize::circos.par()
cell.padding: Passed to circlize::circos.par()
circle.margin: Passed to circlize::circos.par()
facing: Passed to circlize::circos.text()
adj: Passed to circlize::circos.text()
cex: Passed to circlize::circos.text()
...: Additional arguments passed to circlize::chordDiagram()
gg.output: Whether to return the plot as a ggplot object (default is TRUE). If FALSE, an object is not returned; rather the chord diagram is plotted in the graphics device only (default behavior of circlize).