clonalHomeostasis {scRepertoire} | R Documentation

## Examining the clonal homeostasis

### Description

This function calculates the space occupied by clonotype proportions. The grouping of these clonotypes is based on the parameter cloneTypes, at default, cloneTypes will group the clonotypes into bins of Rare = 0 to 0.0001, Small = 0.0001 to 0.001, etc. To adjust the proportions, change the number or labeling of the cloneTypes paramter. If a matrix output for the data is preferred, set exportTable = TRUE.

### Usage

    clonalHomeostasis(
      df,
      cloneTypes = c(Rare = 1e-04, Small = 0.001, Medium = 0.01, Large = 0.1, Hyperexpanded
        = 1),
      cloneCall = "gene+nt",
      exportTable = FALSE
    )

### Arguments

`df` | The product of CombineContig() or expression2List()
`cloneTypes` | The cutpoints of the proportions.
`cloneCall` | How to call the clonotype - CDR3 gene (gene), CDR3 nucleotide (nt) or CDR3 amino acid (aa), or CDR3 gene+nucleotide (gene+nt).
`exportTable` | Exports a table of the data into the global environment in addition to the visualization

### Value

ggplot of the space occupied by the specific propotion of clonotypes

### 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")
    clonalHomeostasis(combined, cloneCall = "gene")

[Package scRepertoire version 1.0.0 Index]