plot_SpaCCI_chordDiagram {SpaCCI} | R Documentation |
This function generates a chord diagram to visualize cell-cell interactions based on ligand-receptor pairs. The interactions can be filtered by specific cell types, pathways, or interaction names.
plot_SpaCCI_chordDiagram(
SpaCCI_Result_List,
specific_celltypes = NULL,
pathway_name = NULL,
L_R_pair_name = NULL,
color = NULL,
alpha = 0.05
)
SpaCCI_Result_List |
A list containing the results from a SpaCCI |
specific_celltypes |
A character vector specifying the cell types to include in the plot, RECOMMEND using colnames of cell type proportion matrix to include all cell types. If |
pathway_name |
A single character string specifying the pathway name to filter the interactions. If |
L_R_pair_name |
A character vector specifying the ligand-receptor pair names to include in the plot. If |
color |
A named vector of colors to use for the cell types. If |
alpha |
A numeric value specifying the significance threshold for adjusted P-values. Initially, set to |
A chord diagram plot visualizing the significant cell-cell interactions.
library(SpaCCI)
library(dplyr)
library(circlize)
data(result_global)
celltypes <- c("beta" , "delta" , "ductal","macrophage",
"activated_stellate", "quiescent_stellate")
# Run the result chordDiagram for global analysis
plot_SpaCCI_chordDiagram(SpaCCI_Result_List = result_global,
specific_celltypes = c(celltypes),
L_R_pair_name = "AREG_EGFR")