getCirclize {scRepertoire} | R Documentation

## Generate data frame to be used with circlize R package to visualize clonotypes as a chord diagram.

### Description

This function will take the meta data from the product of combineExpression()and generate a relational data frame to be used for a chord diagram. The output is a measure of relative clonotype overlap between groups and does not reflect exact clonotype matches between groups.

### Usage

    getCirclize(sc, cloneCall = "gene+nt", groupBy = NULL, proportion = FALSE)

### Arguments

`sc` | object after combineExpression().
`cloneCall` | How to call the clonotype - CDR3 nucleotide (nt), CDR3 amino acid (aa).
`groupBy` | The group header for which you would like to analyze the data.
`proportion` | Binary will calculate relationship as unique clonotypes (proportion = TRUE) or proportion of unique clonotypes (proportion = FALSE)

### Value

data frame of shared clonotypes between groups

### Author(s)

Dillon Corvino, Nick Borcherding

### Examples

    #Getting the combined contigs
    combined <- combineTCR(contig_list, rep(c("PX", "PY", "PZ"), each=2),
    rep(c("P", "T"), 3), cells ="T-AB")

    #Getting a sample of a Seurat object
    screp_example <- get(data("screp_example"))
    screp_example <- combineExpression(combined, screp_example)

    #Getting data frame output for Circilize
    circles <- getCirclize(screp_example, groupBy = "seurat_clusters")

[Package scRepertoire version 1.2.0 Index]