clonalLength: Demonstrate the distribution of clonal length

In ncborcherding/scRepertoire: A toolkit for single-cell immune receptor profiling

Demonstrate the distribution of clonal length

Description

This function displays either the nucleotide (nt) or amino acid (aa) sequence length. The sequence length visualized can be selected using the chains parameter, either the combined clone (both chains) or across all single chains. Visualization can either be a histogram or if scale = TRUE, the output will be a density plot. Multiple sequencing runs can be group together using the group.by parameter.

Usage

clonalLength(
  input.data,
  cloneCall = "aa",
  chain = "both",
  group.by = NULL,
  order.by = NULL,
  scale = FALSE,
  exportTable = FALSE,
  palette = "inferno"
)

Arguments

input.data	The product of combineTCR(), combineBCR(), or combineExpression()
cloneCall	How to call the clone - CDR3 nucleotide (nt) or CDR3 amino acid (aa)
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
order.by	A vector of specific plotting order or "alphanumeric" to plot groups in order description
scale	Converts the graphs into density plots in order to show relative distributions.
exportTable	Returns the data frame used for forming the graph.
palette	Colors to use in visualization - input any hcl.pals

Value

ggplot of the discrete or relative length distributions of clone sequences

Examples

#Making combined contig data
combined <- combineTCR(contig_list, 
                        samples = c("P17B", "P17L", "P18B", "P18L", 
                                    "P19B","P19L", "P20B", "P20L"))
clonalLength(combined, cloneCall="aa", chain = "both")

ncborcherding/scRepertoire documentation built on Nov. 5, 2024, 2:05 p.m.