Selections

Notes on selections:

• Data selections are applied to all plots in a Data viewer sheet if the plots are sharing the data node data plotted. The number of selected points is listed in the Legend on the plot.
• By default, selected points are shown in bold while deselected points are Dim (colors not as bright). Deselected points display can be changed to None or Gray (not colored but instead gray) in the Selections tool in the left panel.
• One bin (cell or grid) can only be in one selection, they can be re-classified when making a new selection.
• An individual selection can be comprised of non-connected regions.

Manual Selections (in-plot tools)

To use the Selections feature, choose it from the left navigation bar

Pointer mode

The most basic way to select a point on is to click it with the mouse while in pointer mode. Click to activate pointer mode if it is not currently active. To select multiple points, you can hold Ctrl on your keyboard and click the cells. To deselect a previously-selected point, hold Ctrl and click it again.

Paint, Lasso, Rectangle, and Ellipse modes

To select larger groups of points, you can switch to Paint, Lasso, Rectangle, and Ellipse modes by clicking the plot controls on the right hand side.

Paint mode

Paint to select points.

• Click to activate Brush mode
• Use the slider at the top of the plot to adjust the brush size
• Click individual sections within the plot
• Click hold and drag the mouse to make larger selections

Lasso mode

Freely draw a shape to select a cluster of points.

• Click to activate Lasso mode
• Left-click and hold to draw a lasso around a cluster of points
• Release and click the starting circle to close the lasso and select the enclosed points

You can also create a lasso with straight lines using Lasso mode by clicking, releasing, and clicking again to draw a shape.

Rectangle mode

Draw a rectangle to select points.

• Click to activate Rectangle mode
• Click the leftmost area to select, hold and drag to complete the rectangle selection

Ellipse mode

Draw an ellipse to select points.

• Click to activate Ellipse mode
• Click the leftmost area to select, then hold and drag the ellipse to cover the area intended for selection

Eraser mode

Use Eraser mode to deselect points that have been previously selected.

• Click to activate Eraser mode
• Use the slider at the top of the plot to adjust the eraser size
• Click to deselect individual points, or click and drag to deselect multiple points

Plot interactivity

The plots in the Spatial report are connected, so making a selection in one will display highlight the selected datapoints in all other plots

For example, the following lasso selection in the UMAP plot highlights just those cells in the other plots.

Click in the white space around any plot to remove the selection.

Saving selections

After points have been selected using a tool, click to save the selection. You will be prompted to label the selection. A point may only belong to one selection at a time; if you save a previously-selected point to a new selection, it will be removed from the first selection.

Saved selections will be listed in the Selections dialog.

Editing saved selections

• Click to edit a selection
• While in edit mode, you can change the selection's label or use any selection mode to add or remove points
• When you are done editing, click to apply your changes, or to discard them

Deleting saved selections

• Click to remove a previously-saved selection

Select & Filter selections

Manual selection mode

A filter can be applied on a selected that has been saved to only include the points within that selection.

• Click on a selection to apply a filter on the selection.
• If a filter has been applied on a selection, click to remove the filter.
• A filter can only be applied on one selection at a time.

Exporting selections

The expression counts for transcripts expressed in points within a selection can be exported and downloaded.

• Click on a selection to start exporting its transcripts.
• The transcripts will be downloaded as a tab-seperated file, with one row per cell/bin and one column per transcript.

Criteria selection mode

Points can be selected using any criteria available for the data node that is selected in the Select & Filter tool.

Data can be dragged directly to Add criteria or use the drop-down to generate selections. When criteria are added, the dialogue will grow with the selections. Remove the selections by clicking .

To change the data selection click the circle (data node) and select the data node which contains the data intended for selection. Ensure the correct data node is selected by hovering on the circle. If not using the intended data node, click the circle and select the data node that contains the information intended for selection. Add criteria for selection contained within the data node.

• If this is a categorial attribute (e.g. clusters), use the check boxes to make a selection.
• If this is a feature expression value a histogram can be used to select expression thresholds. When modifying criteria by low or high values, pin histogram lets you see multiple histograms at a time. Use the slider or manually enter values for selection. Invert can be used to include or exclude selections. Histograms are colored according to selections; dark blue is the current selection, gray is data outside the current selection (i.e. the positions of the slider handles), and light blue is data that is within the slider’s selected region but is currently deselected by other criteria.

Histograms are colored according to selections; dark blue is the current selection, gray is data outside the current selection (i.e. the positions of the slider handles), and light blue is data that is within the slider’s selected region but is currently deselected by other criteria