clonalCompare: Demonstrate the difference in clonal proportions / counts...

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

Demonstrate the difference in clonal proportions / counts between clones

Description

This function produces an alluvial or area graph of the proportion or count composition of the indicated clones for all or selected samples (using the samples parameter). Individual clones can be selected using the clones parameter with the specific sequence of interest or using the top.clones parameter with the top n clones by proportion / counts to be visualized.

Usage

clonalCompare(
  input.data,
  cloneCall = "strict",
  chain = "both",
  samples = NULL,
  clones = NULL,
  top.clones = NULL,
  highlight.clones = NULL,
  relabel.clones = FALSE,
  group.by = NULL,
  order.by = NULL,
  graph = "alluvial",
  proportion = TRUE,
  exportTable = FALSE,
  palette = "inferno"
)

Arguments

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"
samples	The specific samples to isolate for visualization.
clones	The specific clonal sequences of interest
top.clones	The top number of clonal sequences per group. (e.g., top.clones = 5)
highlight.clones	Clonal sequences to highlight, if present, all other clones returned will be grey
relabel.clones	Simplify the legend of the graph by returning clones that are numerically indexed
group.by	If using a single-cell object, the column header to group the new list. NULL will return the active identity or cluster
order.by	A vector of specific plotting order or "alphanumeric" to plot groups in order
graph	The type of graph produced, either "alluvial" or "area"
proportion	If TRUE, the proportion of the total sequencing reads will be used for the y-axis. If FALSE, the raw count will be used
exportTable	Returns the data frame used for forming the graph
palette	Colors to use in visualization - input any hcl.pals

Value

ggplot of the proportion of total sequencing read of selecting clones

Examples

#Making combined contig data
combined <- combineTCR(contig_list,
                       samples = c("P17B", "P17L", "P18B", "P18L",
                                   "P19B","P19L", "P20B", "P20L"))
clonalCompare(combined,
              top.clones = 5,
              samples = c("P17B", "P17L"),
              cloneCall="aa")

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