The next plot is the region viewer.
If you chose the Two cohort comparison starter template, there will be two region viewers—one for each cohort. If you chose the Single cohort starter template, there will be one region viewer.
These panels allow you to visualize the cell type annotations, cell interactions, and Cell Neighborhoods in each of the regions in the cohorts. Clicking on the Cohort Region dropdown allows you to switch which region you are looking at. In the upper right, you can click the Download plot icon to download the plot and legend.
You can toggle between different visualizations by using the Viewer Type dropdown.
Voronoi: This view represents each cell as a voronoi expansion, colored by the cell type or Cell Neighborhood that it belongs to.
Voronoi representations are only available for regions with fewer than 100,000 cells, for performance reasons.
Dot Plot: This view represents each cell as a dot at the cell centroid, colored by the cell type or Cell Neighborhood that it belongs to.
Note that the dot plots are not interactive.
Biomarker Expression Voronoi: This view represents each cell as a voronoi expansion, colored by the biomarker expression of the cell. This view is available if you generated plots using the Biomarker Expression Voronoi Extension in the Analyzer prior to October 2022.
Like the Voronoi above, this visualization is also only available for regions with fewer than 100,000 cells for performance reasons.
Depending on the visualization type, you may also see one or two checkboxes:
Legend: Checking this box will show which colors correspond to which cell types/Cell Neighborhoods
Interactive: Checking this box will allow you to zoom in and out of the plot, and also highlight the cells belonging to each cell type/Cell Neighborhood. Clicking on a cell in the image will highlight all cells of that type, and hovering over each cell type label in the legend will also highlight the cells of that type.
In the Biomarker Expression Voronoi visualization, if you check the Legend and Interactive checkboxes, you can focus visualization to a particular cell type.
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