ClonalKmerPlot

Explore the k-mer frequency of CDR3 sequences.

Usage

ClonalKmerPlot(
  data,
  chain = "TRB",
  clone_call = "aa",
  k = 3,
  top = 25,
  group_by = "Sample",
  group_by_sep = "_",
  facet_by = NULL,
  split_by = NULL,
  plot_type = c("bar", "line", "heatmap"),
  theme_args = list(),
  aspect.ratio = NULL,
  facet_ncol = NULL,
  ...
)

Arguments

data

The product of scRepertoire::combineTCR, scRepertoire::combineTCR, or scRepertoire::combineExpression.

chain

The chain to be analyzed. Default is "TRB".

clone_call

The column name of the clone call. Default is "aa".

k

The length of the k-mer. Default is 3.

top

The number of top k-mers to display. Default is 25.

group_by

The variable to group the data by. Default is "Sample".

group_by_sep

The separator to use when combining groupings. Default is "_".

facet_by

A character vector of column names to facet the plots. Default is NULL.

split_by

A character vector of column names to split the plots. Default is NULL.

plot_type

The type of plot to generate. Default is "bar".

• "bar": Bar plot.

• "line": Line plot.

• "heatmap": Heatmap.

theme_args

A list of arguments to be passed to the ggplot2::theme function.

aspect.ratio

The aspect ratio of the plot. Default is NULL.

facet_ncol

The number of columns in the facet grid. Default is NULL.

...

Other arguments passed to the specific plot function.

• For "bar", plotthis::BarPlot

• For "line", plotthis::LinePlot

• For "heatmap", plotthis::Heatmap

Value

A ggplot object or a list if combine is FALSE

Examples

set.seed(8525)
data(contig_list, package = "scRepertoire")
data <- scRepertoire::combineTCR(contig_list,
    samples = c("P17B", "P17L", "P18B", "P18L", "P19B","P19L", "P20B", "P20L"))
data <- scRepertoire::addVariable(data,
    variable.name = "Type",
    variables = rep(c("B", "L"), 4)
)
data <- scRepertoire::addVariable(data,
    variable.name = "Subject",
    variables = rep(c("P17", "P18", "P19", "P20"), each = 2)
)

ClonalKmerPlot(data)

ClonalKmerPlot(data, group_by = "Type")

ClonalKmerPlot(data, group_by = "Type", plot_type = "line")

ClonalKmerPlot(data, group_by = "Type", plot_type = "heatmap")