Package index • SpaTalk

Object Creation

Create and manage SpaTalk objects

createSpaTalk(): SpaTalk object

SpaTalk SpaTalk-class: Definition of 'SpaTalk' class

show(<SpaTalk>): Show SpaTalk object

Cell-Type Deconvolution

Deconvolve spot-based ST data

dec_celltype(): Decomposing cell type for spatial transcriptomics data

generate_spot(): Generate pseudo spot st_data

set_expected_cell(): Set the expected cell

Cell-Cell Communication

Infer spatially resolved CCIs

find_lr_path(): Find lrpairs and pathways

dec_cci(): Decomposing cell-cell communications for spatial transciptomics data

dec_cci_all(): Decomposing cell-cell communications for spatial transciptomics data

get_lr_path(): Get LR and downstream pathways

Visualization

Plot spatial and CCI results

plot_ccdist(): Plot cell-cell distribution

plot_cci_lrpairs(): Plot LR pairs

plot_lr_path(): Plot LR and downstream pathways

plot_lrpair(): Plot LR pair

plot_lrpair_vln(): Plot spatial distance of LR pair with vlnplot

plot_path2gene(): River plot of significantly activated pathways and related downstream genes of receptors.

plot_st_celltype(): Plot spatial distribution of a single cell type

plot_st_celltype_all(): Plot spatial distribution of all cell types

plot_st_celltype_density(): Plot spatial density of a single cell type

plot_st_celltype_percent(): Plot spatial distribution of a single cell type percent

plot_st_cor_heatmap(): Plot heatpmap of correlation between marker genes and cell types

plot_st_gene(): Plot spatial distribution of gene

plot_st_pie(): Plot spatial transcriptomics data

plot_st_pie_generate(): Plot spatial transcriptomics data

Utilities

Helper functions

rev_gene(): Pre-processing step: revising gene symbols

Data

Built-in databases and demo data

lrpairs: lrpairs

pathways: pathways

geneinfo: geneinfo

demo_dec_result(): Demo data of dec_result

demo_geneinfo(): Demo data of geneinfo

demo_lrpairs(): Demo data of lrpairs

demo_pathways(): Demo data of pathways

demo_sc_data(): Demo data of sc_data

demo_st_data(): Demo data of st_data

demo_st_meta(): Demo data of st_meta

demo_st_sc_data(): Demo data of single-cell st_data

demo_st_sc_meta(): Demo data of st_sc_meta

C++ Functions

Optimized computational routines

cpp_batch_coexp(): Calculate co-expression for multiple gene pairs

cpp_batch_cor(): Calculate correlation between a vector and matrix columns

cpp_coexp_fast(): Calculate co-expression ratios

cpp_fast_dist(): Calculate Euclidean distance matrix

cpp_fast_sampling(): Sample cells to reconstruct spot expression

cpp_knn(): Find K nearest neighbors

cpp_permutation_test(): Permutation test for LR co-expression significance

cpp_random_walk(): Random walk on gene-gene interaction network

Internal

Internal helper functions

SpaTalk SpaTalk-class: Definition of 'SpaTalk' class

cpp_batch_coexp(): Calculate co-expression for multiple gene pairs

cpp_batch_cor(): Calculate correlation between a vector and matrix columns

cpp_coexp_fast(): Calculate co-expression ratios

cpp_fast_dist(): Calculate Euclidean distance matrix

cpp_fast_sampling(): Sample cells to reconstruct spot expression

cpp_knn(): Find K nearest neighbors

cpp_permutation_test(): Permutation test for LR co-expression significance

cpp_random_walk(): Random walk on gene-gene interaction network

createSpaTalk(): SpaTalk object

dec_cci(): Decomposing cell-cell communications for spatial transciptomics data

dec_cci_all(): Decomposing cell-cell communications for spatial transciptomics data

dec_celltype(): Decomposing cell type for spatial transcriptomics data

demo_dec_result(): Demo data of dec_result

demo_geneinfo(): Demo data of geneinfo

demo_lrpairs(): Demo data of lrpairs

demo_pathways(): Demo data of pathways

demo_sc_data(): Demo data of sc_data

demo_st_data(): Demo data of st_data

demo_st_meta(): Demo data of st_meta

demo_st_sc_data(): Demo data of single-cell st_data

demo_st_sc_meta(): Demo data of st_sc_meta

.use_cpp_permutation(): Use Rcpp for fast permutation if available

.use_cpp_random_walk(): Use Rcpp for fast random walk if available

find_lr_path(): Find lrpairs and pathways

geneinfo: geneinfo

generate_spot(): Generate pseudo spot st_data

get_lr_path(): Get LR and downstream pathways

lrpairs: lrpairs

pathways: pathways

plot_ccdist(): Plot cell-cell distribution

plot_cci_lrpairs(): Plot LR pairs

plot_lr_path(): Plot LR and downstream pathways

plot_lrpair(): Plot LR pair

plot_lrpair_vln(): Plot spatial distance of LR pair with vlnplot

plot_path2gene(): River plot of significantly activated pathways and related downstream genes of receptors.

plot_st_celltype(): Plot spatial distribution of a single cell type

plot_st_celltype_all(): Plot spatial distribution of all cell types

plot_st_celltype_density(): Plot spatial density of a single cell type

plot_st_celltype_percent(): Plot spatial distribution of a single cell type percent

plot_st_cor_heatmap(): Plot heatpmap of correlation between marker genes and cell types

plot_st_gene(): Plot spatial distribution of gene

plot_st_pie(): Plot spatial transcriptomics data

plot_st_pie_generate(): Plot spatial transcriptomics data

rev_gene(): Pre-processing step: revising gene symbols

set_expected_cell(): Set the expected cell

show(<SpaTalk>): Show SpaTalk object