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Plot Number or Proportions of Clones

Source: R/clonalQuant.R
clonalQuant.Rd

This function quantifies unique clones. The unique clones can be either reported as a raw output or scaled to the total number of clones recovered using the scale parameter.

Usage

clonalQuant(
  input.data,
  clone.call = NULL,
  chain = "both",
  scale = FALSE,
  group.by = NULL,
  order.by = NULL,
  export.table = NULL,
  palette = "inferno",
  cloneCall = NULL,
  exportTable = NULL,
  ...
)

Arguments

input.data

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

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).

scale

Converts the graphs into percentage of unique clones

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

cloneCall

[Deprecated] Use clone.call instead.

exportTable

[Deprecated] Use export.table instead.

...

Additional arguments passed to the ggplot theme

Value

A ggplot object visualizing the total or relative number 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 clonalQuant()
clonalQuant(combined,
            clone.call="strict",
            scale = TRUE)