Getting Started with SCenic Viewer

Selecting data for plot generation

1. Navigate to the "Apps" section on Bridge Horizon and launch SCenic Viewer by clicking the "Launch" button.
2. Inside SCenic Viewer, click the Browse button under the "Choose a File" section. This opens the file browser. Note that only RDS objects will be available for viewing.
3. Select your RDS object from the available items. SCenic Viewer will attempt to load the RDS object, and once loaded it will automatically populate the UMAP plot.

Remember: SCenic Viewer has no data storage of its own. Upload your data on Bridge Horizon first, then launch SCenic Viewer to access it.

How to generate a UMAP plot

Load an RDS object as described above and the UMAP plot populates automatically. All plots are customized with the features on the right-hand side of your screen. For the UMAP you can adjust:

• Labels: Customize the plot by adjusting labeling, axis titles, and font size.
• Colors: Select a color palette to color the plot. The plot defaults to a polychrome palette.
• Groupings: Choose a grouping method to color cells by Seurat clusters or predefined cell annotations.
• Treatment Split: Select the treatment groupings to facet the UMAP plot and compare cellular responses across experimental conditions.

How to generate a violin plot

Navigate to the Violin Plot tab and enter your genes of interest in the "Genes" text box. SCenic Viewer will search for the genes you entered in your RDS object, and if a gene name is not found, it will automatically search for gene aliases. For instance, if you entered p15ink4b and it is not detected, SCenic Viewer will search for the associated aliases Cdkn2b and Tp15. One plot is generated per gene entered, with expression profiles for each cluster separated along the x-axis.

• Labels: Adjust labeling, axis titles, and font size.
• Groupings: Choose a grouping method to color cells by Seurat clusters or predefined cell annotations.
• Treatment Split: Select treatment groupings to facet the plot and compare cellular responses across conditions.
• Cell Cluster: Limit the plot to the distribution of gene expression in one cell type of interest only.

How to generate a feature plot

Navigate to the Feature Plot tab and enter your genes of interest in the "Genes" text box. As with the violin plot, if a gene name is not found, SCenic Viewer will automatically search for gene aliases. One plot is generated per gene entered. Feature plots can also be generated for specific groups or clusters, and often include density representations for an overall view of expression distribution.

• Labels: Adjust labeling, axis titles, and font size.
• Quantile Cutoff: Adjust the upper and lower quantile cutoffs to filter gene expression levels, focusing on specific expression ranges by excluding extreme values.
• Treatment Split: Select a treatment type to facet the UMAP plot and compare cellular distributions and gene expression profiles across conditions.

How to leverage advanced features and save your session

Beyond generating plots, SCenic Viewer lets you fine-tune every visual. For example:

• Resize any plot canvas by clicking and holding the small triangle at its bottom right-hand corner and dragging.
• Change fonts, styles, and axis titles from the "Label" menu in the right sidebar (the sidebar may be pushed below the plot canvas depending on your browser window size).
• Switch the UMAP color palette from the "Colors" menu. See the full plot descriptions for guidance on reading each chart type.

To keep your work, save your SCenic Viewer session and return to it later. The "How to Save Your Session" video in the video tutorial library walks through it.

How to download plots

1. Rename the export via the text box under the "File Name" section (the default placeholder is "example_filename").
2. Click the blue download button above the plot canvas, beside the "File Name" section, to download a high-resolution image in PNG, JPG, SVG, or PDF format.