The cirrocumulus interface consists of an app bar, side bar, primary embedding, embedding gallery and toolbar, distribution plots, and differential expression results explorer.


Primary embedding

The primary view is an interactive 2 or 3-dimensional embedding:


For spatial data, you can overlay genes or cell metadata on top of an image:


Interact with the view:

  • Pan: Mouse left click (2-d), right click (3-d)

  • Hover: Hover a data point to see the underlying value

  • Rotate 3-d: Mouse left click

  • Zoom: Mouse wheel

  • Select: When using lasso or select tool, hold down the Ctrl or Command key to add to selection

  • Resize: Click and drag the divider below the primary embedding

  • Tooltip: Mouse move

  • Select Category: Mouse double-click


The primary embedding view enables fast, interactive exploration of 1.3 million cells. Note that higher values are plotted on top of lower values for genes, whereas categorical values are plotted in random order:


You can interactively annotate clusters (optionally using a controlled vocabulary), and include positive and negative cluster markers:



Use the toolbar to change the active tool. The lasso and brush tools allow you to visually select cells of interest:


The “Append to selection” button controls whether the lasso and brush tools append to the selection.

Click the label button to toggle the visibility of categorical labels directly on the embedding:


In a 3-d plot, use the play button to rotate the plot in a loop.


and toggle whether to fade distant points or to show a 3-d axis:


Additional buttons include saving the embedding image to svg or png.


The “Distributions” tab allows users to explore gene distributions across cell categories using dot plots, heatmaps, or violin plots:


When selecting more than one category, the plot first groups by the primary category, then by the secondary category, etc. For example, when you select “leiden” and “sample”, the plot first groups by leiden cluster and then by sample.

Additionally, a composition plot shows categorical distributions:


App Bar

The app bar shows the number of cells in your dataset and the number of selected cells. Additionally, it lets you switch between different tabs.

Share your visualization state with your collaborators by selecting “Copy Link” from the “More” menu.