Alluvial Plotting for Single-Cell Object

Source: R/alluvialClones.R

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.

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

Arguments

sc.data

The product of combineExpression().

cloneCall

Defines the clonal sequence grouping. Accepted values are: gene (VDJC genes), nt (CDR3 nucleotide sequence), aa (CDR3 amino acid sequence), or strict (VDJC + nt). A custom column header can also be used.

chain

The TCR/BCR chain to use. Use both to include both chains (e.g., TRA/TRB). Accepted values: TRA, TRB, TRG, TRD, IGH, IGL (for both light chains), both.

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

If TRUE, returns a data frame or matrix of the results instead of a plot.

palette

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

...

Additional arguments passed to the ggplot theme

Value

A ggplot object visualizing categorical distribution of clones, or a data.frame if exportTable = TRUE.

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")