chord_diagram {barcodetrackR} | R Documentation

## Barcode Chord Diagram

### Description

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.

### Usage

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

### Arguments

`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.

### Value

Displays a chord diagram in the current plot window depicting shared clonality between samples (regions) as chords or links between the regions. Or,

### Examples

    data(wu_subset)
    chord_diagram(your_SE = wu_subset[, c(4, 8, 12)], plot_label = "celltype")

[Package barcodetrackR version 1.2.0 Index]