ClonalOverlapPlot

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

Usage

ClonalOverlapPlot(
  data,
  clone_call = "aa",
  chain = "both",
  group_by = "Sample",
  group_by_sep = "_",
  full = TRUE,
  split_by = NULL,
  order = list(),
  method = c("raw", "overlap", "morisita", "jaccard", "cosine"),
  palette = "Blues",
  label_accuracy = NULL,
  label_cutoff = 0.001,
  cluster_rows = FALSE,
  cluster_columns = FALSE,
  show_row_names = TRUE,
  show_column_names = TRUE,
  ...
)

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"

group_by

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

group_by_sep

The separator used to concatenate the group_by when multiple columns are used.

full

Whether to plot the full heatmap, or just a triangle. Default is TRUE.

split_by

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

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.

method

The method to calculate the overlap. Default is "raw".

• "overlap" - overlap coefficient

• "morisita" - Morisita’s overlap index

• "jaccard" - Jaccard index

• "cosine" - cosine similarity

• "raw" - exact number of overlapping clones See also scRepertoire::clonalOverlap.

palette

The color palette to use. Default is "Blues".

label_accuracy

The accuracy of the labels. Default is NULL. If NULL, it will be 1 for "raw" and 0.01 for other methods.

label_cutoff

The cutoff for the labels to show. Default is 1e-3.

cluster_rows

Whether to cluster the rows. Default is FALSE.

cluster_columns

Whether to cluster the columns. Default is FALSE.

show_row_names

Whether to show the row names. Default is TRUE.

show_column_names

Whether to show the column names. Default is TRUE.

...

Other arguments passed to the specific plot function plotthis::Heatmap.

Value

A ComplexHeatmap 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)
)

ClonalOverlapPlot(data)

ClonalOverlapPlot(data, clone_call = "strict", label_cutoff = 0,
  label_accuracy = 0.001, method = "morisita", full = FALSE)

ClonalOverlapPlot(data, group_by = c("Subject", "Type"))

ClonalOverlapPlot(data, group_by = "Type", split_by = "Subject")