make_circos_lr: make_circos_lr

In saeyslab/nichenetr: NicheNet: Modeling Intercellular Communication by Linking Ligands to Target Genes

make_circos_lr

Description

make_circos_lr Plot the prioritized ligand-receptor pairs in a circos plot (via the circlize package)

Usage

make_circos_lr(
  prioritized_tbl_oi,
  colors_sender,
  colors_receiver,
  cutoff = 0,
  scale = FALSE,
  transparency = NULL,
  circos_type = "normal",
  border = TRUE,
  separate_legend = FALSE
)

Arguments

prioritized_tbl_oi	Dataframe with the ligand-receptor interactions that should be visualized
colors_sender	Named character vector giving the colors of each sender cell type
colors_receiver	Named character vector giving the colors of each receiver cell type
cutoff	Threshold On the prioritization score - if lower than this value, the link will be removed – default = 0.
scale	scale value in 'chordDiagram'. Default: FALSE
transparency	Vector of transparency values of the links or NULL, in that case this will be calculated automatically. Default: NULL.
circos_type	"normal" or "arrow". Default: "normal".
border	Border to arrows or not in 'chordDiagram'? (Default: TRUE)
separate_legend	return plot and legend as separate objects? (Default: FALSE)

Value

List containing the circos plot and the legend

Examples

## Not run: 
make_circos_lr(prioritized_tbl_oi, colors_sender, colors_receiver, cutoff = 0, scale = FALSE, transparency = NULL, circos_type = "normal", border = TRUE)

## End(Not run)

saeyslab/nichenetr documentation built on April 27, 2024, 9:24 p.m.