alluvialClones: Alluvial plotting for single-cell object meta data

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

Alluvial plotting for single-cell object meta data

Description

View the proportional contribution of clones by Seurat or SCE object meta data after combineExpression. The visualization is based on the ggalluvial package, which requires the aesthetics to be part of the axes that are visualized. Therefore, alpha, facet, and color should be part of the the axes you wish to view or will add an additional stratum/column to the end of the graph.

Usage

alluvialClones(
  sc.data,
  cloneCall = "strict",
  chain = "both",
  y.axes = NULL,
  color = NULL,
  alpha = NULL,
  facet = NULL,
  exportTable = FALSE,
  palette = "inferno"
)

Arguments

sc.data	The single-cell object to visualize after 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".
y.axes	The columns that will separate the proportional . visualizations.
color	The column header or clone(s) to be highlighted.
alpha	The column header to have gradated opacity.
facet	The column label to separate.
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.

Value

Alluvial ggplot comparing clone distribution.

Examples

#Getting the combined contigs
combined <- combineTCR(contig_list, 
                        samples = c("P17B", "P17L", "P18B", "P18L", 
                                    "P19B","P19L", "P20B", "P20L"))

#Getting a sample of a Seurat object
scRep_example <- get(data("scRep_example"))

#Using combineExpresion()
scRep_example <- combineExpression(combined, scRep_example)
scRep_example$Patient <- substring(scRep_example$orig.ident, 1,3)

#Using alluvialClones()
alluvialClones(scRep_example, 
                   cloneCall = "gene", 
                   y.axes = c("Patient", "ident"), 
                   color = "ident")

ncborcherding/scRepertoire documentation built on April 27, 2024, 8:34 p.m.