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ClonalDiversityPlot

Source: R/clonaldivplot.R
ClonalDiversityPlot.Rd

Plot the clonal diversities of the samples/groups.

Usage

ClonalDiversityPlot(
  data,
  clone_call = "gene",
  chain = "both",
  method = c("shannon", "gini.coeff", "inv.simpson", "norm.entropy", "gini.simpson",
    "chao1", "ACE", "d50", "dXX"),
  d = 50,
  plot_type = c("bar", "box", "violin"),
  position = "dodge",
  group_by = NULL,
  facet_by = NULL,
  split_by = NULL,
  xlab = NULL,
  ylab = NULL,
  ...
)

Arguments

data

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

clone_call

How to call the clone - VDJC gene (gene), CDR3 nucleotide (nt), CDR3 amino acid (aa), VDJC gene + CDR3 nucleotide (strict) or a custom variable in the data

chain

indicate if both or a specific chain should be used - e.g. "both", "TRA", "TRG", "IGH", "IGL"

method

The method to calculate the diversity. Options are "shannon" (default), "inv.simpson", "norm.entropy", "gini.simpson", "chao1", "ACE", "gini.coeff", "d50" and "dXX". See scRepertoire::clonalDiversity for details. The last 3 methods are supported by scplotter only:

  • "gini.coeff" - The Gini Coefficient. A measure of inequality in the distribution of clones. 0 indicates perfect equality, 1 indicates perfect inequality.

  • "d50" - The number of clones that make up 50% of the total number of clones.

  • "dXX" - The number of clones that make up XX% of the total number of clones.

d

The percentage for the "dXX" method. Default is 50.

plot_type

The type of plot. Options are "bar", "box" and "violin".

position

The position adjustment for the bars. Default is "dodge".

group_by

A character vector of column names to group the samples. Default is NULL.

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.

xlab

The x-axis label. Default is NULL.

ylab

The y-axis label. Default is NULL.

...

Other arguments passed to the specific plot function.

  • For "bar", plotthis::BarPlot

  • 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)
)
data <- scRepertoire::addVariable(data,
    variable.name = "Subject",
    variables = rep(c("P17", "P18", "P19", "P20"), each = 2)
)

ClonalDiversityPlot(data)

ClonalDiversityPlot(data, group_by = "Type")

ClonalDiversityPlot(data, group_by = "Type", plot_type = "box")

ClonalDiversityPlot(data, group_by = "Type", plot_type = "violin")

ClonalDiversityPlot(data, group_by = "Type", plot_type = "violin",
  method = "gini.coeff", add_box = TRUE)

ClonalDiversityPlot(data, group_by = "Type", plot_type = "violin",
  method = "inv.simpson", add_box = TRUE)

ClonalDiversityPlot(data, group_by = "Type", plot_type = "violin",
  method = "d50", add_box = TRUE)