ClonalAbundancePlot

Plot the count or density of the clones at different abundance levels.

Usage

ClonalAbundancePlot(
  data,
  clone_call = "aa",
  chain = "both",
  xtrans = "log10",
  ytrans = "identity",
  plot_type = c("trend", "histogram", "density"),
  binwidth = 0.1,
  trend_skip_zero = TRUE,
  bw = 0.5,
  group_by = "Sample",
  group_by_sep = "_",
  facet_by = NULL,
  split_by = NULL,
  order = list(),
  xlab = "Abundance",
  ylab = NULL,
  theme_args = list(),
  ...
)

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"

xtrans

The transformation to apply to the x-axis. Default is "log10".

ytrans

The transformation to apply to the y-axis. Default is "identity".

plot_type

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

binwidth

The binwidth for the histogram plot. Default is 0.1.

trend_skip_zero

Whether to skip the zero values in the trend line. Default is TRUE.

bw

The smoothing bandwidth to be used for density plots. Default is 0.5.

group_by

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

group_by_sep

The separator to use when combining the group_by columns. Default: "_"

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

order

The order of the x-axis items or 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. Default is "Abundance".

ylab

The y-axis label. Default is "Number of Clones" for trend and histogram, and "Density of Clones" for density.

theme_args

The theme arguments to be passed to the plot function.

...

Other arguments passed to the specific plot function.

• For trend plot, see plotthis::Histogram.

• For histogram plot, see plotthis::Histogram.

• For density plot, see plotthis::DensityPlot.

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)
)

ClonalAbundancePlot(data)
#> Warning: Removed 104 rows containing missing values or values outside the scale range
#> (`geom_line()`).

ClonalAbundancePlot(data, ytrans = "log10")
#> Warning: log-10 transformation introduced infinite values.
#> Warning: Removed 104 rows containing missing values or values outside the scale range
#> (`geom_line()`).

ClonalAbundancePlot(data, plot_type = "histogram")

ClonalAbundancePlot(data, plot_type = "histogram", add_trend = TRUE, trend_skip_zero = TRUE)
#> Warning: Removed 104 rows containing missing values or values outside the scale range
#> (`geom_line()`).

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