`R/positionalEntropy.R`

`positionalEntropy.Rd`

This function the diversity amino acids along the residues
of the CDR3 amino acid sequence. Please see
`clonalDiversity`

for more information on
the underlying methods for diversity/entropy calculations.
Positions without variance will have a value reported as 0
for the purposes of comparison.

```
positionalEntropy(
input.data,
chain = "TRB",
group.by = NULL,
order.by = NULL,
aa.length = 20,
method = "norm.entropy",
exportTable = FALSE,
palette = "inferno"
)
```

- input.data
The product of

`combineTCR`

,`combineBCR`

, or`combineExpression`

- chain
"TRA", "TRB", "TRG", "TRG", "IGH", "IGL"

- group.by
The variable to use for grouping

- order.by
A vector of specific plotting order or "alphanumeric" to plot groups in order

- aa.length
The maximum length of the CDR3 amino acid sequence.

- method
The method to calculate the entropy/diversity - "shannon", "inv.simpson", "norm.entropy"

- exportTable
Returns the data frame used for forming the graph

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

ggplot of line graph of diversity by position

```
#Making combined contig data
combined <- combineTCR(contig_list,
samples = c("P17B", "P17L", "P18B", "P18L",
"P19B","P19L", "P20B", "P20L"))
positionalEntropy(combined,
chain = "TRB",
aa.length = 20)
```