ClonalGeneUsagePlot

ClonalGeneUsagePlot

Usage

ClonalGeneUsagePlot(
  data,
  genes = "TRBV",
  scale = TRUE,
  top = 20,
  plot_type = c("bar", "heatmap", "circos", "chord", "alluvial", "sankey"),
  group_by = "Sample",
  facet_by = NULL,
  facet_ncol = 1,
  split_by = NULL,
  aspect.ratio = 2/top,
  theme_args = list(),
  ylab = NULL,
  row_annotation = NULL,
  row_annotation_type = list(),
  row_annotation_side = "right",
  row_annotation_agg = list(),
  ...
)

Arguments

data

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

genes

The prefix of genes to be plotted. Default is "TRBV". If two sets of genes are provided (e.g. c("TRBV", "TRBJ")), the second dimension will be the second set of genes instead of the group_by variable.

scale

Whether to use the proportion that is scaled to the group or the count.

top

The number of top genes/genepairs to be plotted.

plot_type

The type of plot to be generated. Default is "bar". Options are "bar", "heatmap", "circos" (aka "chord").

group_by

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

facet_by

A character vector of column names to facet the plots. Default is NULL. Should not be specified manually.

facet_ncol

The number of columns in the facet grid. Default is 1.

split_by

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

aspect.ratio

The aspect ratio of the plot. Only available for "bar" plot. Default is 2/top.

theme_args

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

ylab

The y-axis label. Default is NULL.

row_annotation

A list of row annotations to be added to the heatmap. Default is NULL.

row_annotation_type

A list of row annotation types.

row_annotation_side

The side of the row annotation. Default is "right".

row_annotation_agg

A list of row annotation aggregation functions.

...

Other arguments passed to the specific plot function.

• For "bar", plotthis::BarPlot

• For "heatmap", plotthis::Heatmap

• For "circos", plotthis::ChordPlot

• For "chord", plotthis::ChordPlot

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)
)

ClonalGeneUsagePlot(data)

ClonalGeneUsagePlot(data, genes = "TRBJ", genes2 = "TRBV")

ClonalGeneUsagePlot(data, top = 40, plot_type = "heatmap")

ClonalGeneUsagePlot(data, genes = c("TRBV", "TRBJ"), plot_type = "heatmap")

ClonalGeneUsagePlot(data, genes = "TRBV", group_by = "Type", plot_type = "chord")

ClonalGeneUsagePlot(data, genes = c("TRBV", "TRBJ"), group_by = "Type", plot_type = "chord")

ClonalGeneUsagePlot(data, genes = c("TRBV", "TRBJ"), plot_type = "alluvial")