# Spatial Interaction Markers

## Documentation for package ‘SpaceMarkers’ version 2.3.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A C D F G H I L O P S U misc

## -- A --

add_features | Add spatial features to a SpaceMarkersExperiment
analysis_type | Access or set the analysis type on a SpaceMarkersExperiment
analysis_type-method | Access or set the analysis type on a SpaceMarkersExperiment
analysis_type<- | Access or set the analysis type on a SpaceMarkersExperiment
analysis_type<--method | Access or set the analysis type on a SpaceMarkersExperiment
as-SingleCellExperiment-SpaceMarkersExperiment | Coercion from SingleCellExperiment to SpaceMarkersExperiment
as-SpatialExperiment-SpaceMarkersExperiment | Coercion from SpatialExperiment to SpaceMarkersExperiment

## -- C --

calculate_gene_scores_directed | Calculate interaction scores for all pattern pairs
calculate_gene_scores_directed-method | Calculate interaction scores for all pattern pairs
calculate_gene_set_score | calculate_gene_set_score
calculate_gene_set_score-method | calculate_gene_set_score
calculate_gene_set_specificity | calculate_gene_set_specificity
calculate_gene_set_specificity-method | calculate_gene_set_specificity
calculate_influence | Compute the spatial influence of a spatial feature
calculate_influence-method | Compute the spatial influence of a spatial feature
calculate_lr_scores | calculate_lr_scores
calculate_lr_scores-method | calculate_lr_scores
calculate_overlap_directed | calculate_overlap_directed
calculate_overlap_directed-method | calculate_overlap_directed
calculate_overlap_undirected | calculate_overlap_undirected
calculate_overlap_undirected-method | calculate_overlap_undirected
calculate_thresholds | Compute the thresholds for all columns in a data frame
create_lr_dataframe | Combine LR / ligand / receptor score matrices into a long table
curated_genes | Curated Genes for example purposes

## -- D --

directed_scores | Access directed interaction scores on a SpaceMarkersExperiment
directed_scores-method | Access directed interaction scores on a SpaceMarkersExperiment
directed_scores<- | Access directed interaction scores on a SpaceMarkersExperiment
directed_scores<--method | Access directed interaction scores on a SpaceMarkersExperiment

## -- F --

find_all_hotspots | Find hotSpots for all spatial patterns
find_all_hotspots-method | Find hotSpots for all spatial patterns
find_hotspots_gmm | Find hotspots for all patterns or influences based on values
find_hotspots_gmm-method | Find hotspots for all patterns or influences based on values
find_pattern_hotspots | Identify hotspots of spatial pattern influence

## -- G --

get_im_scores | get_im_scores
get_im_scores-method | get_im_scores
get_interacting_genes | Calculate Interaction Regions and Associated Genes
get_pairwise_interacting_genes | get_pairwise_interacting_genes
get_pairwise_interacting_genes-method | get_pairwise_interacting_genes
get_spatial_features | Load spatial features
get_spatial_parameters | Read optimal parameters for spatial kernel density from user input or .json file
get_spatial_params_morans_i | Calculate the optimal parameters from spatial kernel density for cell-cell interactions

## -- H --

hotspots | Access hotspot assignments on a SpaceMarkersExperiment
hotspots-method | Access hotspot assignments on a SpaceMarkersExperiment
hotspots<- | Access hotspot assignments on a SpaceMarkersExperiment
hotspots<--method | Access hotspot assignments on a SpaceMarkersExperiment

## -- I --

influence_map | Access the per-spot influence map on a SpaceMarkersExperiment
influence_map-method | Access the per-spot influence map on a SpaceMarkersExperiment
influence_map<- | Access the per-spot influence map on a SpaceMarkersExperiment
influence_map<--method | Access the per-spot influence map on a SpaceMarkersExperiment
interactions | Access pairwise interaction results on a SpaceMarkersExperiment
interactions-method | Access pairwise interaction results on a SpaceMarkersExperiment
interactions<- | Access pairwise interaction results on a SpaceMarkersExperiment
interactions<--method | Access pairwise interaction results on a SpaceMarkersExperiment

## -- L --

load10X | Load 10X Visium data as a SpaceMarkersExperiment
load10XCoords | Load 10x Visium Spatial Coordinates
load10XExpr | Load 10X Visium Expression Data
load_anndata | Load an AnnData file as a SpaceMarkersExperiment
lrdf | Curated Ligand-receptor interaction genes A list of vectors with genes associated with ligand-receptor interactions from CellChat database
lr_scores | Access ligand-receptor scores on a SpaceMarkersExperiment
lr_scores-method | Access ligand-receptor scores on a SpaceMarkersExperiment
lr_scores<- | Access ligand-receptor scores on a SpaceMarkersExperiment
lr_scores<--method | Access ligand-receptor scores on a SpaceMarkersExperiment

## -- O --

optParams | Optimal paramters of 5 patterns from CoGAPS.
overlap_map | Per-spot overlap classification map for a pattern pair
overlap_scores | Access pattern overlap scores on a SpaceMarkersExperiment
overlap_scores-method | Access pattern overlap scores on a SpaceMarkersExperiment
overlap_scores<- | Access pattern overlap scores on a SpaceMarkersExperiment
overlap_scores<--method | Access pattern overlap scores on a SpaceMarkersExperiment

## -- P --

params | Access analysis hyperparameters on a SpaceMarkersExperiment
params-method | Access analysis hyperparameters on a SpaceMarkersExperiment
plot_cell_interaction_circos | Plot Ligand-Receptor Interactions between Cell Types
plot_im_scores | plot_im_scores
plot_overlap_scores | plot_overlap_scores
plot_source_to_target_circos | Plot Ligand-Receptor Interactions from a Single Source to Target Cell Types
plot_spatial | plot_spatial
plot_spatial_data_over_image | plotSpatialDataOverImage
plot_target_from_sources_circos | Plot Ligand-Receptor Interactions from Multiple Source to a Single Target Cell Type

## -- S --

save_anndata | Save a SpaceMarkersExperiment as an AnnData (.h5ad) file
show-method | SpaceMarkersExperiment class
SpaceMarkers | Main dispatcher for SpaceMarkers
SpaceMarkersExperiment | Create a SpaceMarkersExperiment object
SpaceMarkersExperiment-accessors | Accessor generics for SpaceMarkersExperiment
SpaceMarkersExperiment-class | SpaceMarkersExperiment class
spatial_params | Access or set the spatial-kernel parameters on a SpaceMarkersExperiment
spatial_params-method | Access or set the spatial-kernel parameters on a SpaceMarkersExperiment
spatial_params<- | Access or set the spatial-kernel parameters on a SpaceMarkersExperiment
spatial_params<--method | Access or set the spatial-kernel parameters on a SpaceMarkersExperiment
spatial_patterns | Accessor generics for SpaceMarkersExperiment
spatial_patterns-method | Accessor generics for SpaceMarkersExperiment
spatial_patterns<- | Accessor generics for SpaceMarkersExperiment
spatial_patterns<--method | Accessor generics for SpaceMarkersExperiment

## -- U --

undirected_scores | Access undirected interaction scores on a SpaceMarkersExperiment
undirected_scores-method | Access undirected interaction scores on a SpaceMarkersExperiment
undirected_scores<- | Access undirected interaction scores on a SpaceMarkersExperiment
undirected_scores<--method | Access undirected interaction scores on a SpaceMarkersExperiment

## -- misc --

.calc_IM_scores | Calculate interaction scores for a specific pattern pair
.calc_threshold | Compute the threshold for identifying outlier values or hotspots
.directed_SpaceMarkers | Directed SpaceMarkers workflow
.find_genes_of_interest | .find_genes_of_interest Identify genes associated with pattern interaction. This function identifies genes exhibiting significantly higher values of testMat in the Interaction region of the two patterns compared to regions with exclusive influence from either pattern. It uses Kruskal-Wallis test followed by posthoc analysis using Dunn's Test to identify the genes.
.pick_image | .pick_image
.row_t_test | Perform row-wise t-tests from scratch
.undirected_SpaceMarkers | Undirected SpaceMarkers workflow