Overview | Installation | Setup | Links to Data | Downloading Data | Loading Data into a SpaceMarkersExperiment | Filtering | Accessors | Undirected Analysis | Step 0: Visualize the starting patterns | Step 1: Find hotspots | Step 2: Calculate overlap scores | Step 3: Find pairwise interacting genes | Step 4: Calculate IM scores | Directed Analysis | Step 1: Calculate influence | Step 2: Find pattern hotspots | Step 3: Find influence hotspots | Step 4: Directed overlap scores | Step 5: Directed gene scores | Putting it together | Cleanup | Session Info

Overview | Installation | Setup | Links to Data | Downloading Data | Loading Data into a SpaceMarkersExperiment | Using load10X | Filtering | Running SpaceMarkers with the SME Object | Undirected Analysis | Inspecting Results | Directed Analysis | Visualization | Patterns on the tissue | Undirected hotspots | Undirected overlap scores | Undirected interaction overlay | IM scores bar plot and top genes | Directed hotspots | Directed overlap scores | Directed interaction overlays | Constructing a SpaceMarkersExperiment Manually | From an Existing SpatialExperiment | Backward Compatibility | Summary | Cleanup | Session Info

Overview | Installation | Setup | Links to Data | Extracting Counts Matrix | load10xExpr | Obtaining CoGAPS Patterns | Obtaining Spatial Coordinates | load10XCoords | Executing SpaceMarkers | SpaceMarker Modes | Residual Mode | SpaceMarkers Step1: Hotpsots | SpaceMarkers Step2: Interacting Genes | DE Mode | Residual Mode vs DE Mode: Differences | Comparing residual mode to DE mode | Comparing DE mode to residual mode | Types of Analyses | Residual Mode vs DE Mode: Enrichment | Visualizing SpaceMarkers | Loading Packages | Code Setup | Get the Spatial Data | Generate Plots | Pattern_1 | Pattern_5 | Top SpaceMarkers | Negative SpaceMarkersMetric | Removing Directories | References | load10XExpr() Arguments | load10XCoords() Arguments | get_spatial_params_morans_i() Arguments | get_pairwise_interacting_genes() Arguments

Importing Local Libraries | Preparing the Data | Creating a Basic ScatterHatch Plot | Customizing ScatterHatch Plot | Changing the Order of Pattern Assignment | Changing the Angles of each Pattern | scatterHatch() Arguments Explained | Pattern Aesthetics Arguments | Session Info