ClonalPositionalPlot

Visualize the positional entropy, property or amino acid frequency of CDR3 sequences.

Usage

ClonalPositionalPlot(
  data,
  chain = "TRB",
  aa_length = 20,
  group_by = "Sample",
  group_by_sep = "_",
  split_by = NULL,
  method = c("AA", "shannon", "inv.simpson", "norm.entropy", "Atchley", "Kidera",
    "stScales", "tScales", "VHSE"),
  plot_type = c("bar", "line", "heatmap", "box", "violin"),
  theme_args = list(),
  xlab = NULL,
  ylab = NULL,
  facet_by = NULL,
  facet_ncol = NULL,
  facet_nrow = NULL,
  aspect.ratio = NULL,
  ...
)

Arguments

data

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

chain

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

aa_length

The length of the amino acid sequence. Default is 20.

group_by

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

group_by_sep

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

split_by

The variable to split the data by. Default is NULL.

method

The method to calculate the positional entropy. Default is "AA".

• "AA": Amino acid frequency.

• "shannon": Shannon entropy.

• "inv.simpson": Inverse Simpson index.

• "norm.entropy": Normalized entropy.

• "Atchley": Atchley factors.

• "Kidera": Kidera factors.

• "stScales": stScales factors.

• "tScales": tScales factors.

• "VHSE": Vectors of Hydrophobic, Steric, and Electronic properties. See also scRepertoire::percentAA, scRepertoire::positionalEntropy and scRepertoire::positionalProperty.

plot_type

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

• "bar": Bar plot.

• "line": Line plot.

• "heatmap": Heatmap.

• "box": Box plot.

• "violin": Violin plot.

theme_args

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

xlab

The x-axis label. Default is NULL.

ylab

The y-axis label. Default is NULL.

facet_by

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

facet_ncol

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

facet_nrow

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

aspect.ratio

The aspect ratio of the plot. Default is NULL.

...

Other arguments passed to the specific plot function.

• For "bar", plotthis::BarPlot

• For "line", plotthis::LinePlot

• For "heatmap", plotthis::Heatmap

• For "box", plotthis::BoxPlot

• For "violin", plotthis::ViolinPlot

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)
)

ClonalPositionalPlot(data)

ClonalPositionalPlot(data, method = "shannon")

ClonalPositionalPlot(data, method = "norm.entropy", plot_type = "heatmap")

ClonalPositionalPlot(data, method = "Atchley", group_by = "Type", plot_type = "bar")

ClonalPositionalPlot(data, method = "Atchley", plot_type = "line")