diff --git a/R/plot_fxns.R b/R/plot_fxns.R index d41f16b..6bfe16a 100644 --- a/R/plot_fxns.R +++ b/R/plot_fxns.R @@ -785,7 +785,7 @@ circos_ligand_receptor <- function( ) # render circos plot render_circos_ligand_receptor( - signaling_df = signaling_df, + signaling_df = signaling_df, receptor = receptor, cell_colors = cell_colors, cell_idents = cell_idents, ligand_expression_threshold = ligand_expression_threshold ) @@ -855,6 +855,7 @@ obtain_circos_expression <- function(dom, receptor, ligands, ligand_expression_t #' Renders a circos plot from the output of [obtain_circos_expression()] to the active graphics device #' #' @param signaling_df Data frame output from [obtain_circos_expression()] +#' @param receptor Name of a receptor active in at least one cell type in the domino object #' @param ligand_expression_threshold Minimum mean expression value of a ligand by a cell type for a chord to be rendered between the cell type and the receptor #' @param cell_idents Vector of cell types from cluster assignments in the domino object to be included in the plot. #' @return a circlize plot is rendered to the active graphics device @@ -867,10 +868,9 @@ obtain_circos_expression <- function(dom, receptor, ligands, ligand_expression_t #' render_circos_ligand_receptor <- function( - signaling_df, cell_colors = NULL, cell_idents = NULL, ligand_expression_threshold = 0.01 + signaling_df, receptor, cell_colors = NULL, cell_idents = NULL, ligand_expression_threshold = 0.01 ){ ligands <- sort(unique(signaling_df$ligand)) - receptor <- sort(unique(signaling_df$receptor)) # colors for ligand chords lig_colors <- ggplot_col_gen(length(ligands)) names(lig_colors) <- ligands