Examining the relative composition of kmer motifs in clones.

Source: R/percentKmer.R

This function the of kmer for nucleotide (nt) or amino acid (aa) sequences. Select the length of the kmer to quantify using the motif.length parameter.

percentKmer(
  input.data,
  chain = "TRB",
  cloneCall = "aa",
  group.by = NULL,
  order.by = NULL,
  motif.length = 3,
  top.motifs = 30,
  exportTable = FALSE,
  palette = "inferno"
)

Arguments

input.data

The product of combineTCR(), combineBCR(), or combineExpression()

chain

"TRA", "TRB", "TRG", "TRG", "IGH", "IGL"

cloneCall

How to call the clone - CDR3 nucleotide (nt) or CDR3 amino acid (aa)

group.by

The variable to use for grouping

order.by

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

motif.length

The length of the kmer to analyze

top.motifs

Return the n most variable motifs as a function of median absolute deviation

exportTable

Returns the data frame used for forming the graph.

palette

Colors to use in visualization - input any hcl.pals

Value

ggplot of percentage of kmers as a heatmap

Examples

#Making combined contig data
combined <- combineTCR(contig_list, 
                        samples = c("P17B", "P17L", "P18B", "P18L", 
                                    "P19B","P19L", "P20B", "P20L"))
percentKmer(combined, 
            chain = "TRB", 
            motif.length = 3)