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Plot the Clonal Space Occupied by Specific Clones

Source: R/clonalProportion.R
clonalProportion.Rd

This function calculates the relative clonal space occupied by the clones. The grouping of these clones is based on the parameter clonalSplit, at default, clonalSplit will group the clones into bins of 1:10, 11:100, 101:1001, etc. To adjust the clones selected, change the numbers in the variable split. If a matrix output for the data is preferred, set exportTable = TRUE.

Usage

clonalProportion(
  input.data,
  clonal.split = NULL,
  clone.call = NULL,
  chain = "both",
  group.by = NULL,
  order.by = NULL,
  export.table = NULL,
  palette = "inferno",
  clonalSplit = NULL,
  cloneCall = NULL,
  exportTable = NULL,
  ...
)

Arguments

input.data

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

clonal.split

The cut points for the specific clones, default = c(10, 100, 1000, 10000, 30000, 1e+05)

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

clonalSplit

[Deprecated] Use clonal.split instead.

cloneCall

[Deprecated] Use clone.call instead.

exportTable

[Deprecated] Use export.table instead.

...

Additional arguments passed to the ggplot theme

Value

A ggplot object dividing space occupied by ranks of clones or a data.frame if exportTable = TRUE.

Examples

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