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 run_SpaCCI(..., analysis_scale = "local",...) `dataframelist`

RegionIDs_matrix

A result of matrix list from the output of run_SpaCCI(..., analysis_scale = "local",...) `RegionIDs_matrix`

celltype_ligand

Ligand cell type string inputted by user, the name of the cell type should match the names in the `spot_cell_proportion_dataframe` during the run_SpaCCI analysis.

celltype_receptor

Receptor cell type string inputted by user, the name of the cell type should match the names in the `spot_cell_proportion_dataframe` during the run_SpaCCI analysis.

plot_size

As this function incorporate with Seurat's `SpatialFeaturePlot`, this parameter could control the plotting size of the each spot.

L_R_pair_name

Initially this is set to NULL, if one is interested in a specific Ligand-Receptor pair, then one could specify the L_R_pair_name here. Note: the input name should match the L-R pair name exists in the dataframe in the output of SpaCCI_local "dataframelist".

alpha

This is the significant cutoff for the adjusted-p-value of thr permutation test. Initially this is set to 0.05, one could adjust the cutoff.

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)



[Package SpaCCI version 1.0.4 Index]