`R/clonalRarefaction.R`

`clonalRarefaction.Rd`

This functions uses the Hill numbers of order q: species richness (**q = 0**),
Shannon diversity (**q = 1**), the exponential of Shannon entropy and Simpson
diversity (**q = 2**, the inverse of Simpson concentration) to compute diversity
estimates for rarefaction and extrapolation. The function relies on the
`iNEXT`

R package. Please read and cite the
manuscript
if using this function. The input into the iNEXT calculation is abundance,
incidence-based calculations are not supported.

```
clonalRarefaction(
input.data,
cloneCall = "strict",
chain = "both",
group.by = NULL,
plot.type = 1,
hill.numbers = 0,
n.boots = 20,
exportTable = FALSE,
palette = "inferno"
)
```

- input.data
The product of

`combineTCR`

,`combineBCR`

, or`combineExpression`

.- cloneCall
How to call the clone - VDJC gene (

**gene**), CDR3 nucleotide (**nt**), CDR3 amino acid (**aa**), VDJC gene + CDR3 nucleotide (**strict**) or a custom variable in the data.- chain
indicate if both or a specific chain should be used - e.g. "both", "TRA", "TRG", "IGH", "IGL".

- group.by
The variable to use for grouping.

- plot.type
sample-size-based rarefaction/extrapolation curve (

`type = 1`

); sample completeness curve (`type = 2`

); coverage-based rarefaction/extrapolation curve (`type = 3`

).- hill.numbers
The Hill numbers to be plotted out (0 - species richness, 1 - Shannon, 2 - Simpson)

- n.boots
The number of bootstraps to downsample in order to get mean diversity.

- exportTable
Exports a table of the data into the global environment in addition to the visualization.

- palette
Colors to use in visualization - input any hcl.pals.

```
#Making combined contig data
combined <- combineTCR(contig_list,
samples = c("P17B", "P17L", "P18B", "P18L",
"P19B","P19L", "P20B", "P20L"))
clonalRarefaction(combined[c(1,2)], cloneCall = "gene", n.boots = 3)
```