abundanceContig {scRepertoire} | R Documentation

## Demonstrate the relative abundance of clonotypes by group or sample.

### Description

This function takes the output of combineTCR(), combineBCR(), or expression2List() and displays the number of clonotypes at specific frequencies by sample or group. Visualization can either be a line graph using calculated numbers or if scale = TRUE, the output will be a density plot. Multiple sequencing runs can be group together using the group parameter. If a matrix output for the data is preferred, set exportTable = TRUE.

### Usage

    abundanceContig(
      df,
      cloneCall = "gene+nt",
      scale = FALSE,
      group = NULL,
      exportTable = FALSE
    )

### Arguments

`df` | The product of combineTCR(), combineBCR(), or expression2List().
`cloneCall` | How to call the clonotype - CDR3 gene (gene), CDR3 nucleotide (nt), CDR3 amino acid (aa), or C DR3 gene+nucleotide (gene+nt).
`scale` | Converts the graphs into denisty plots in order to show relative distributions.
`group` | The column header for which you would like to analyze the data.
`exportTable` | Returns the data frame used for forming the graph to the visualization.

### Value

ggplot of the total or relative adundance of clonotypes across quanta

### 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")
    abundanceContig(combined, cloneCall = "gene", scale = FALSE)

[Package scRepertoire version 1.2.0 Index]