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Plot the Relative Abundance of Clones

Source: R/clonalAbundance.R
clonalAbundance.Rd

Displays the number of clones at specific frequencies by sample or group. Visualization can either be a line graph ( scale = FALSE) using calculated numbers or density plot (scale = TRUE). Multiple sequencing runs can be group together using the group parameter. If a matrix output for the data is preferred, set export.table = TRUE.

Usage

clonalAbundance(
  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 density plots in order to show relative distributions.

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 clonal abundance by group, or a data.frame if export.table = TRUE.

Author

Nick Borcherding, Justin Reimertz

Examples

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

# Using clonalAbundance()
clonalAbundance(combined,
                clone.call = "gene",
                scale = FALSE)