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ClonalCompositionPlot

Source: R/clonalstatplot.R
ClonalCompositionPlot.Rd

Plot the composition of the clones in different samples/groups.

Usage

ClonalCompositionPlot(
  data,
  clone_call = "aa",
  chain = "both",
  method = c("homeostasis", "homeo", "rel", "top", "rare"),
  clone_split = NULL,
  scale = TRUE,
  facet_by = NULL,
  group_by = NULL,
  split_by = NULL,
  xlab = NULL,
  ylab = NULL,
  plot_type = c("bar", "ring", "box", "violin"),
  order = 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"

method

The method of plot to use. Default is "homeostasis". Possible values are "homeostasis", "homeo", "rel", "top", and "rare".

  • "homeostasis" - Plot the homeostasis/relative abundance of the clones. The clone_split will be the fraction of the clones in each sample.

  • "homeo" - Same as "homeostasis".

  • "rel" - Same as "homeostasis".

  • "top" - Plot the top clones. The clone_split will be indexes to cut the clones.

  • "rare" - Plot the rare clones. The clone_split will be the clone sizes.

clone_split

The split for the clones. Default is NULL.

  • For "homeostasis", "homeo", "rel" - Default is list(Rare = 1e-04, Small = 0.001, Medium = 0.01, Large = 0.1, Hyperexpanded = 1).

  • For "top" - Default is c(10, 100, 1000, 10000, 30000, 100000).

  • For "rare" - Default is c(1, 3, 10, 30, 100).

scale

Whether to scale the values on the y-axis. Default is TRUE.

  • TRUE: The values of each group (on the x-axis) will be scaled to 1.

  • FALSE: No scaling.

  • "sample"/"Sample": The values in each sample will be scaled to 1.

facet_by

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

group_by

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

split_by

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

xlab

The x-axis label. Default is NULL.

ylab

The y-axis label. Default is NULL.

plot_type

The type of plot to use. Default is "bar". Possible values are "bar", "ring", "box", and "violin".

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.

...

Other arguments passed to the specific plot function.

  • For bar plot, see plotthis::BarPlot.

  • For ring plot, see plotthis::RingPlot.

  • 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,
    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)
)

ClonalCompositionPlot(data)

ClonalCompositionPlot(data, method = "top")

ClonalCompositionPlot(data, plot_type = "ring")

ClonalCompositionPlot(data, group_by = "Type", plot_type = "box", comparison = TRUE)

ClonalCompositionPlot(data, group_by = "Type", plot_type = "violin", add_box = TRUE,
 add_bg = TRUE)

ClonalCompositionPlot(data, method = "rare")