prepare_circos_visualization: Prepare circos visualization

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

Prepare circos visualization

Description

Prepare the data for the circos visualization by incorporating the colors and order of the links, as well as gaps between different cell types

Usage

prepare_circos_visualization(circos_links, ligand_colors = NULL, target_colors = NULL, widths = NULL, celltype_order = NULL)

Arguments

circos_links	Dataframe from the function get_ligand_target_links_oi containing weighted ligand-target links, cell type expressing the ligand, and target gene goruping
ligand_colors	Named vector of colors for each cell type (default: NULL, where colors follow the ggplot default color scheme)
target_colors	Named vector of colors for each target gene grouping (default: NULL, where colors follow the ggplot default color scheme)
widths	Named list of widths for the different types groupings, including: width_same_cell_same_ligand_type: Width of the links between ligands of the same cell type (default: 0.5) width_different_cell: Width of the links between different cell types, or between different target gene groups (default: 6) width_ligand_target: Width of the links between ligands and targets (default: 15) width_same_cell_same_target_type: Width of the links between target genes of the same group (default: 0.5)
celltype_order	Order of the cell types (default: NULL, where cell types are ordered alphabetically, followed by "General"). Cell types are then drawn counter-clockwise in the circos plot.

Value

A list of four objects, including:

• circos_links: Dataframe of weighted ligand-target links

• ligand_colors: Named vector of ligands and their colors

• order: Vector of order of the ligands and target genes

• gaps: Vector of gaps between the different groupings

Examples

## Not run: 
celltype_order <- c("General", "NK", "B", "DC", "Mono")
ligand_colors <- c("General" = "lawngreen", "NK" = "royalblue", "B" = "darkgreen", "Mono" = "violet", "DC" = "steelblue2")
target_colors <- c("LCMV-DE" = "tomato")
vis_circos_obj <- prepare_circos_visualization(circos_links, ligand_colors, target_colors, celltype_order = celltype_order)

## End(Not run)

saeyslab/nichenetr documentation built on Sept. 7, 2024, 10:27 a.m.