Sender-by-receiver heatmap of CCI scores for one ligand-receptor pair

Generic function. Reshapes the CCI data frame into a receiver-by-sender cell-type matrix for one selected LR pair and draws a clustered heatmap.

Usage

plotCCILR(x, ...)

# S3 method for class 'blisa'
plotCCILR(x, index = 1, ligand = NULL, receptor = NULL, main = NULL, ...)

# Default S3 method
plotCCILR(x, lr_pair, main = NULL, ...)

Arguments

x

A blisa object or a CCI scores data frame (the CCI_scores slot of a blisa object).

...

Additional arguments passed to the relevant method.

index

Integer. Row index into LR_results selecting the ligand-receptor pair to visualise. Ignored when both ligand and receptor are supplied. Default 1 (top-ranked pair).

ligand

Character. Ligand gene symbol. When both ligand and receptor are provided the matching LR pair is located automatically and index is ignored. Must be supplied together with receptor.

receptor

Character. Receptor gene symbol. Must be supplied together with ligand.

main

Character or NULL. Title drawn above the heatmap. When supplied, the heatmap is drawn with this overall title (via ComplexHeatmap::draw); the Heatmap object is returned invisibly. Default NULL (no title; object returned for the caller to print).

lr_pair

Character. Column name in the CCI scores data frame corresponding to the ligand-receptor pair to visualise (e.g. "CXCL12_CXCR4").

Value

A Heatmap object.

Methods (by class)

• plotCCILR(blisa): Method for a blisa object. The LR pair is selected by index (default 1, the top-ranked pair) unless both ligand and receptor are supplied, in which case the matching row is located automatically and index is ignored. Stops with an informative error if CCI_scores is NULL or the selected LR pair has no significant hotspots.

• plotCCILR(default): Method for a CCI scores data frame (e.g. the CCI_scores slot of a blisa object). The LR pair is selected by column name via lr_pair.

See also

plotCCI for an overview heatmap across all LR pairs; plotCCIsummary for an aggregated sender-by-receiver heatmap.

Examples

if (FALSE) { # \dontrun{
# Continuing from the blisa() example:
# result <- blisa(spe, bin_size = 50, group = "cell_type")
plotCCILR(result, index = 1)
} # }