clonalDiversity {scRepertoire} | R Documentation

## Examine the clonal diversity of samples

### Description

This function calculates traditional measures of diversity - Shannon, inverse Simpson, Chao1 index, and abundance-based coverage estimators (ACE) by sample or group. The group paramter can be used to condense the individual samples. If a matrix output for the data is preferred, set exportTable = TRUE.

### Usage

    clonalDiversity(
      df,
      cloneCall = "gene+nt",
      group = "samples",
      exportTable = FALSE
    )

### Arguments

`df` | The product of combineTCR(), combineBCR(), or expression2List().
`cloneCall` | How to call the clonotype - CDR3 gene (gene), CDR3 nucleotide (nt) or CDR3 amino acid (aa), or CDR3 gene+nucleotide (gene+nt).
`group` | The column header for which you would like to analyze the data.
`exportTable` | Exports a table of the data into the global environment in addition to the visualization

### Value

ggplot of the diversity of clonotype sequences across list

### Examples

    #Making combined contig data
    x <- contig_list
    combined <- combineTCR(x, rep(c("PX", "PY", "PZ"), each=2),
    rep(c("P", "T"), 3), cells ="T-AB")
    clonalDiversity(combined, cloneCall = "gene")

[Package scRepertoire version 1.2.0 Index]