Grouped chord diagrams

Grouped chord diagrams

Usage

plotCohortChordDiagram(
  object,
  nn,
  feature,
  group.1,
  group.2 = NULL,
  color.pal = NULL,
  ...
)

Arguments

object

A SpatialMap object

nn

The name of a nearestNeighborGraph from object (character).

feature

The name of a cellMetadata column (character).

group.1

Vector of Region names, or a column name in projectMetadata used for grouping. If a projectMetadata column name is passed, group.2 should be NULL. In this case, for each categorical level in the given column, two cohorts are defined:

1. All regions matching that categorical level in the specified projectMetadata column

2. All regions not matching that level

group.2

Vector of Region names. If NULL, looks in projectMetadata for a column name matching group.1 to create cohorts.

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")

...

Arguments passed on to plot_chord_diagram

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()