4. Cell cluster plot
UMAP plot of 18 tissues from the Tabula Muris compendium.
The plot was generated from the input expression matrix in RNA-Scoop.
The cell cluster plot is generated from the input expression matrix, or, if it has been loaded, the input embedding file (see the Input file formats section for details). To draw the cell cluster plot, press the "Draw cell plot" button. The algorithm used to generate the cell cluster plot is determined by the cluster view settings dialogue. Users can choose to use either the UMAP or t-SNE, and tune the parameters for each algorithm. If you edited the cluster view settings, press the "OK" button to draw the cell cluster plot with these settings. If you close the dialogue or press the "Draw cell plot" button before pressing the "OK" button, or edits will not be saved, and the cell cluster plot will be generated using the previous algorithm settings.
The cluster view settings dialogue
The cell cluster plot is interactive, allowing users to zoom in/out of different areas and pan the plot freely. To zoom into an area, put your mouse over that area and scroll towards yourself. Similarly to zoom out, scroll away from yourself. To pan the plot, hold down the control key and click and drag the cursor.
Cells are selectable via lasso selection. To select a group of cells, click and drag your cursor to create a lasso selection shape. After releasing the cursor, all cells that were in that shape will be selected. To select additional cells, hold down shift when you click and drag the mouse. When cells are selected, the isoforms in the isoform view are calculated based on their expression in the selected cells only, and the dot plot is generated from the selected cells only as well. For more information on this, see the Isoform view section. To select all cells of a specific cell category, click on the category name in the legend. To select cells from multiple cell categories, hold down shift when clicking.
Zooming, panning and selecting cells in the cell cluster plot
The cell cluster plot supports multiple label sets. See the Label set manager section for details.
If the cell cluster plot is drawn, the embedding that it is currently being displayed can be exported to a file. To do this, press the "Export embedding" button. The exported embedding file will be in the same format as the input embedding file format (see the Input file formats section for details).