Spatial Data Viewer

The Spatial Report includes:

• The tissue image with cell or grid bin spatial data overlay
• The UMAP plot colored by cluster
• A pie chart representing the clusters

The coordinates for the spatial image correspond to the original flow cell.

The data opens to the cell binned data Spatial report. The graphs are based on the cell binned data and colored by Leiden clusters. To change the colors, see Configuring Spatial Images. The tissue image has the cells overlaid, so if you zoom in to the tissue image, you will see the individual cells.

The grid binned Spatial report has plots based on the grid binned data. This will include all transcripts in the sample, as it includes the space between cells. The tissue image is initially colored by total count of transcripts. To change the colors, see Configuring Spatial Images.

The Task Graph

To navigate to the task graph, click on the sample name just above the left menu:

The task graph displays analysis output from the DRAGEN StrataMap software. The defaults are for cell binned data and 10µm grid binned data. Additional sizes of grid binned data, if generated, will populate here as well.

To navigate back to the cell spatial report from the task graph, double click the 'spatial report' downstream of the "Spatial - Cells" data node. The spatial report downstream of the "Spatial - Grids" data node will take you to the grid binned spatial report.