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Prepare circos visualization

Source: R/application_visualization.R
prepare_circos_visualization.Rd

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

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

if (FALSE) { # \dontrun{
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)
} # }