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Plot Clonal Homeostasis of the Repertoire

Source: R/clonalHomeostasis.R
clonalHomeostasis.Rd

This function calculates the space occupied by clone proportions. The grouping of these clones is based on the parameter clone.size, at default, clone.size will group the clones into bins of Rare = 0 to 0.0001, Small = 0.0001 to 0.001, etc. To adjust the proportions, change the number or labeling of the clone.size parameter. If a matrix output for the data is preferred, set export.table = TRUE.

Usage

clonalHomeostasis(
  input.data,
  clone.size = NULL,
  clone.call = NULL,
  chain = "both",
  group.by = NULL,
  order.by = NULL,
  export.table = NULL,
  palette = "inferno",
  cloneSize = NULL,
  cloneCall = NULL,
  exportTable = NULL,
  ...
)

Arguments

input.data

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

clone.size

The cut points of the proportions.

clone.call

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, IGK, Light (for both light chains), or both (for TRA/B and Heavy/Light).

group.by

A column header in the metadata or lists to group the analysis by (e.g., "sample", "treatment"). If NULL, data will be analyzed by list element or active identity in the case of single-cell objects.

order.by

A character vector defining the desired order of elements of the group.by variable. Alternatively, use alphanumeric to sort groups automatically.

export.table

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.

cloneSize

[Deprecated] Use clone.size instead.

cloneCall

[Deprecated] Use clone.call instead.

exportTable

[Deprecated] Use export.table instead.

...

Additional arguments passed to the ggplot theme

Value

A ggplot object visualizing clonal homeostasis, or a data.frame if export.table = TRUE.

Examples

# Making combined contig data
combined <- combineTCR(contig_list,
                        samples = c("P17B", "P17L", "P18B", "P18L",
                                    "P19B","P19L", "P20B", "P20L"))
clonalHomeostasis(combined, clone.call = "gene")