plot_localized_Seurat {SpaCCI} | R Documentation |
Plot Localized Hotspot Pattern on Seurat Object
Description
Visualize the inferred cell-cell interaction localized pattern on the tissue image with Seurat_object
Usage
plot_localized_Seurat(
Seurat_object,
resultdf_list,
RegionIDs_matrix,
celltype_ligand,
celltype_receptor,
plot_size,
L_R_pair_name = NULL,
alpha = 0.05
)
Arguments
Seurat_object |
A Seurat object |
resultdf_list |
A result of data frame list from the output of |
RegionIDs_matrix |
A result of matrix list from the output of |
celltype_ligand |
Ligand cell type string inputted by user, the name of the cell type should match the names in the |
celltype_receptor |
Receptor cell type string inputted by user, the name of the cell type should match the names in the |
plot_size |
As this function incorporate with |
L_R_pair_name |
Initially this is set to |
alpha |
This is the significant cutoff for the adjusted-p-value of thr permutation test. Initially this is set to |
Value
The localized plot from the inferred cell-cell interaction on the local scale.
Examples
# Not Run
# Run localized hotspot plot
Result <- run_SpaCCI(..., analysis_scale = "local",...)
local_plot <- plot_localized_Seurat(Seurat_object = gene_spot_df,
resultdf_list = Result$dataframelist,
RegionIDs_matrix = Result$RegionIDs_matrix,
celltype_ligand = "Beta_cells",
celltype_receptor = "T_ells",
plot_size = 3)