Get started with SpatialMap

SpatialMap’s interactive user journey

If you have a Workbench subscription, you can work with these notebooks interactively by accessing the source code in your home directory, in the folder spatialmap_vignettes. On this website, we demonstrate the capabilities of the SpatialMap package using example datasets.

For help logging in to Workbench, and other questions about computing on workbench, see our platform user manual or our Workbench tutorial videos.

Get started

To get a brief overview of the elements of the SpatialMap package, you can start here:

vignette("Quickstart_guide")

This is a good place to start if you’re already an expert in R and spatial biology analysis.

Analysis Guide vignettes

If you’d like a more detailed walkthrough of the core functionalities of SpatialMap, and guidance for your spatial biology analysis, see the Analysis Guide vignettes. These vignettes demonstrate many facets of a standard workflow using SpatialMap, and can also serve as a starting point for analyzing your own dataset.

1. vignette("AnalysisGuide1_Loading_sm_object_from_ATLAS")

2. vignette("AnalysisGuide2_QC_with_SpatialMap")

3. vignette("AnalysisGuide3_Unsupervised_clustering")

4. vignette("AnalysisGuide4_Subsetting_and_subclustering")

5. vignette("AnalysisGuide5_Cell_interactions")

6. vignette("AnalysisGuide6_Neighborhoods")

7. vignette("AnalysisGuide7_Cohort_comparison")

Advanced tutorials

For tips on more advanced work with SpatialMap, see our tutorial vignettes.

• vignette("Tutorial_Troubleshooting_SpatialMap")

• vignette("Tutorial_Annotations_to_Portal")

• vignette("Tutorial_Plots_to_Portal")

• vignette("Tutorial_Plotting_with_SpatialMap")

• vignette("Tutorial_Accessing_slots_in_SpatialMap_object")

• vignette("Tutorial_Manipulating_SpatialMap_objects")

• vignette("Tutorial_Advanced_spatial")

• vignette("Tutorial_Exporting_Data")