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Scatter Plot Comparing Clones Across Two Samples

Source: R/clonalScatter.R
clonalScatter.Rd

This function produces a scatter plot directly comparing the specific clones between two samples. The clones will be categorized by counts into singlets or expanded, either exclusive or shared between the selected samples.

Usage

clonalScatter(
  input.data,
  clone.call = NULL,
  x.axis = NULL,
  y.axis = NULL,
  chain = "both",
  dot.size = "total",
  group.by = NULL,
  graph = "proportion",
  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.

x.axis

name of the list element to appear on the x.axis.

y.axis

name of the list element to appear on the y.axis.

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).

dot.size

either total or the name of the list element to use for size of dots.

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.

graph

graph either the clonal "proportion" or "count".

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 dynamics between two groupings 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 clonalScatter()
clonalScatter(combined, 
              x.axis = "P17B", 
              y.axis = "P17L",
              graph = "proportion")