Cirrocumulus is an interactive visualization tool for large-scale single-cell and spatial transcriptomic data. The data visualization page consists of five parts: a section selector, a top toolbar, a sidebar, a main canvas, and a gallery.

  • The section selector on the top allows users to select a specific section in the dataset.
  • The top toolbar displays the number of cells and the number of selected cells in the dataset on the left. The right part has three buttons: EMBEDDINGS, DISTRIBUTIONS, and a moon symbol. The EMBEDDINGS button shows the default canvas interface. The DISTRIBUTIONS option allows users to explore the differential gene expression across cell clusters with a dot plot, a heat map, or a violin plot. The moon symbol button is the dark model option.

  • The left sidebar allows you to select genes/traits to be visualized, select clustering tags, and run differential expression analysis.

  • The main canvas shows an interactive 2d or 3D graphic, which can be panned, zoomed, and selected in specific regions using the mouse.

  • The gallery, which locates in the bottom, shows thumbnails of selected genes/gene sets. Users can click the thumbnail to display it on the main canvas.

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How to use

it will show the spatial map of corresponding gene in different dataset sections when user select the species and gene in the page of toll. User also can click the section name to enter the corresponding dataset visualization for more details.