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