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ClonalVolumePlot

Source: R/clonalstatplot.R
ClonalVolumePlot.Rd

ClonalVolumePlot

Usage

ClonalVolumePlot(
  data,
  clone_call = "aa",
  chain = "both",
  scale = FALSE,
  plot_type = c("bar", "box", "violin"),
  x = "Sample",
  group_by = NULL,
  facet_by = NULL,
  split_by = NULL,
  order = list(),
  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"

scale

Whether to use clone proportion or clone size for the plot.

plot_type

The type of plot to use. Default is "bar". Possible values are "bar", "box", and "violin". When "box" or "violin" is used, the data will be broken down by the Sample and plotted for each group.

x

The column name in the meta data to use as the x-axis. Default: "Sample"

group_by

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

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.

ylab

The y-axis label.

...

Other arguments passed to the specific plot function.

  • For bar plot, see plotthis::BarPlot.

  • For box plot, see plotthis::BoxPlot.

  • For violin plot, see 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)
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)
)

ClonalVolumePlot(data)

ClonalVolumePlot(data, x = "Type")

ClonalVolumePlot(data, x = "Type", order = list(Type = c("L", "B")))

ClonalVolumePlot(data, x = c("Type", "Sex"), scale = TRUE)
#> Multiple columns are provided in 'x'. They will be concatenated into one column.

ClonalVolumePlot(data, x = "Type", group_by = "Sex", position = "stack")

ClonalVolumePlot(data,
    plot_type = "box", x = "Type", comparisons = TRUE,
    group_by = "Sex"
)

ClonalVolumePlot(data, plot_type = "violin", x = "Type", add_box = TRUE)


# on a Seurat object
data(scRep_example, package = "scRepertoire")
data(contig_list, package = "scRepertoire")
combined <- scRepertoire::combineTCR(contig_list,
    samples = c("P17B", "P17L", "P18B", "P18L", "P19B", "P19L", "P20B", "P20L")
)
sobj <- scRepertoire::combineExpression(combined, scRep_example)
ClonalVolumePlot(sobj)
#> Warning: The 'Sample' column is not found in the meta data, 'orig.indent' will be used instead.

ClonalVolumePlot(sobj, x = "seurat_clusters")
#> Warning: The 'Sample' column is not found in the meta data, 'orig.indent' will be used instead.

ClonalVolumePlot(sobj, group_by = "seurat_clusters")
#> Warning: The 'Sample' column is not found in the meta data, 'orig.indent' will be used instead.

ClonalVolumePlot(sobj, x = "seurat_clusters", plot_type = "box")
#> Warning: The 'Sample' column is not found in the meta data, 'orig.indent' will be used instead.