scE file format

Single cell Embroider requires scRNA-seq data from Seurat. Following is the list of information required to load New Data in scE:

• Gene List
• Sub-clustering Information
• Distribution mapping
• Gene Expression Matrix

scE files can be saved in .mat files, which only requires one file and it stores images and gene list from scE. To load .mat files, click Load Data.

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How to use scE

Above is from heart.mat file which is included in scE download link. It can be loaded from Embroider > application > Mat > heart.mat file.

1. Gene

scE can show up to 15 genes at the same time for easier visualization. To change the gene list, click Set Gene, enter genes of interest and click apply.

All on and All off buttons make it easier to view the entire gene list. By clicking individual genes, you can decide whether to view them or not.

2. Clusters

scE offers two different dimension reduction options: tSNE and UMAP. Sliders at the bottom of plots and images allow users to easily change the size of each dot as well as the opacity of the background plot/image.

3. Images

scE can be used to visualize scRNA-seq cluster data on any images (tissue image, cartoons, spatial transcriptomics image, etc.). To change the image, click Set Image.

There will be a list of cell types. Click Load Image to upload an image.

Click □ or ○ to select a region of the image and click the pencil icon to choose the color in the selected region. Repeat this step for each cell types. Click Apply to insert image.

4. Violin plot

scE automatically creates two violin plots. To view the violin plot for a certain cell type, click the drop-down menu and select a cell type of interest.