chord_diagram: Barcode Chord Diagram
In d93espinoza/barcodetrackR: Functions for Analyzing Cellular Barcoding Data

Description Usage Arguments Value Examples

Creates a chord diagram showing each cell type (or other factor) as a region around a circle and shared clones between these cell types as links between the regions. The space around the regions which is not connected to a chord indicates clones unique to that sample, not shared with other samples.

chord_diagram(
  your_SE,
  weighted = FALSE,
  plot_label = "SAMPLENAME",
  alpha = 1,
  your_title = NULL,
  text_size = 12,
  return_table = FALSE
)

`your_SE`	Summarized Experiment object containing clonal tracking data as created by the barcodetrackR 'create_SE' function.
`weighted`	Logical. weighted = F which is default will make links based on the number of shared clones between the factors. Weighted = TRUE will make the link width based on the clone's proportion in the samples.
`plot_label`	Character. Name of colData variable to use as labels for regions. Defaults to SAMPLENAME
`alpha`	Numeric. Transparency of links. Default = 1 is opaque. 0 is completely transluscent
`your_title`	Character. The title for the plot.
`text_size`	Numeric. Size of region labels
`return_table`	Logical. If set to TRUE, in addition to plotting a chord diagram in the plot window, the function will return a dataframe of the shared clonality used to make the chord diagram. If Weighted is FALSE, the dataframe will contain a row for each set of clones and values of 1 or 0 indicating the samples which share that set of clones, and a freq column which is the number of clones in that set. If weighted is set to TRUE, each row will contain a set of clones and the data will show the proportion that set of clones comprises in each sample. The proportions of 0 indicate which samples do not share that set of clones.