ClonalLengthPlot

Plot the length distribution of the CDR3 sequences

Usage

ClonalLengthPlot(
  data,
  clone_call = "aa",
  chain = "both",
  plot_type = c("bar", "box", "violin", "density"),
  x_nbreaks = 10,
  group_by = "Sample",
  order = list(),
  xlab = "Length",
  ylab = NULL,
  position = "dodge",
  facet_by = NULL,
  split_by = NULL,
  ...
)

Arguments

data

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

clone_call

How to call the clone - only "nt" or "aa" is supported.

chain

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

plot_type

The type of plot to use. Default is "bar". Possible values are "histogram" and "density".

x_nbreaks

The number of breaks for the x-axis. Default is 10.

group_by

The column name in the meta data to group the cells. Default: "Sample"

order

The order of the groups. Default is an empty list. It should be a list of values. The names are the column names, and the values are the order.

xlab

The x-axis label.

ylab

The y-axis label.

position

The position of the bars for bar plot on the x-axis. Default is "dodge".

facet_by

The column name in the meta data to facet the plots. Default: NULL

split_by

The column name in the meta data to split the plots. Default: NULL

...

Other arguments passed to the specific plot function.

• For

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)
data <- scRepertoire::addVariable(data, variable.name = "Type",
 variables = sample(c("B", "L"), 8, replace = TRUE))
data <- scRepertoire::addVariable(data, variable.name = "Sex",
 variables = sample(c("M", "F"), 8, replace = TRUE))

ClonalLengthPlot(data)

ClonalLengthPlot(data, plot_type = "box")

ClonalLengthPlot(data, clone_call = "nt", plot_type = "violin", chain = "TRB",
 group_by = "Type", comparisons = TRUE)
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.
#> Warning: Groups with fewer than two datapoints have been dropped.
#> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.

ClonalLengthPlot(data, plot_type = "density", chain = "TRA")
#> Using `bins = 30`. Pick better value with `binwidth`.