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Plot the Distribution of Sequence Lengths

Source: R/clonalLength.R
clonalLength.Rd

This function displays either the nucleotide nt or amino acid aa sequence length. The sequence length visualized can be selected using the chains parameter, either the combined clone (both chains) or across all single chains. Visualization can either be a histogram or if scale = TRUE, the output will be a density plot. Multiple sequencing runs can be group together using the group.by parameter.

Usage

clonalLength(
  input.data,
  clone.call = NULL,
  chain = "both",
  group.by = NULL,
  order.by = NULL,
  scale = FALSE,
  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: nt (CDR3 nucleotide sequence) or aa (CDR3 amino acid sequence)

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.

scale

Converts the graphs into density plots in order to show relative distributions.

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 distributions by length, 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"))
clonalLength(combined, clone.call = "aa", chain = "both")