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Heatmap of CCI scores across all ligand-receptor pairs

Source: R/plotCCI.R
plotCCI.Rd

Generic function. Draws a clustered heatmap (via ComplexHeatmap) with rows as Sender \(\rightarrow\) Receiver cell-type pairs and columns as LR pairs. Row annotations colour-code the sender and receiver cell types.

Usage

plotCCI(x, ...)

# S3 method for class 'blisa'
plotCCI(
  x,
  top_lr = 20,
  top_pairs = 30,
  lr_pairs = NULL,
  sender = NULL,
  receiver = NULL,
  colors = NULL,
  colours = NULL,
  main = NULL,
  ...
)

# Default S3 method
plotCCI(
  x,
  top_lr = 20,
  top_pairs = 30,
  lr_pairs = NULL,
  sender = NULL,
  receiver = NULL,
  colors = NULL,
  colours = NULL,
  main = NULL,
  ...
)

Arguments

x

A blisa object or a CCI scores data frame (the CCI_scores slot of a blisa object). The data frame must contain columns Sender, Receiver, and one column per LR pair.

...

Additional arguments passed to the relevant method.

top_lr

Integer or NULL. Number of top-ranked LR pairs (by sig_numbers) to display as columns. LR pairs in CCI_scores are already ordered by rank, so this simply takes the first top_lr columns. Ignored when lr_pairs is supplied. Default 20.

top_pairs

Integer or NULL. Number of top sender-receiver pairs to display as rows, ranked by their maximum interaction score across the displayed LR pairs (after top_lr / lr_pairs is applied). When NULL all rows are shown. Default 30.

lr_pairs

Character vector or NULL. When supplied, only these LR pair column names are shown, in the order given, overriding top_lr. Names not found in CCI_scores are dropped with a warning. Default NULL (use top_lr).

sender

Character vector or NULL. If provided, only rows where Sender is in this vector are kept. Applied independently of receiver (AND logic when both are supplied). Default NULL (all senders).

receiver

Character vector or NULL. If provided, only rows where Receiver is in this vector are kept. Applied independently of sender (AND logic when both are supplied). Default NULL (all receivers).

colors

Named character vector mapping cell-type names to colours, used for the sender/receiver row annotations. When NULL (default), colours are assigned automatically from the package palette. The British spelling colours is accepted as an alias.

colours

Alias for colors (British spelling). Ignored when colors is supplied.

main

Character or NULL. Title drawn above the heatmap (mapped to the column_title of ComplexHeatmap::Heatmap). Default NULL (no title).

Value

Invisibly returns the Heatmap object.

Methods (by class)

  • plotCCI(blisa): Method for a blisa object. Extracts CCI_scores and delegates to plotCCI.default. Stops with an informative error if CCI_scores is NULL.

  • plotCCI(default): Method for a CCI scores data frame (e.g. the CCI_scores slot of a blisa object).

See also

plotCCILR for a sender-by-receiver heatmap of a single LR pair; plotCCIsummary for an aggregated sender-by-receiver heatmap across all LR pairs.

Examples

if (FALSE) { # \dontrun{
# Continuing from the blisa() example:
# result <- blisa(spe, bin_size = 50, group = "cell_type")
plotCCI(result, top_lr = 20, top_pairs = 30)
} # }