SingleCellTK provides a general portal for cell level visualization, including the functionality to create scatter plot, bar plot, and violin plot. Users should find the Cell Viewer as instructed in the screenshot above. This documentation will start with a quick example and then talk about the detail.
Here we provide a common case of plotting a UMAP with clusters labeled. We take the frequently used “PBMC3k” dataset, provided by 10X, as an example. The detailed screenshot for each prerpocessing step will not be included, but users can refer to the documentation of those steps within other pages.
In Cell Viewer:
The procedure of creating a single plot in Cell Viewer can be generalized as three steps: axis selection, color specification, and peripheral setting.
In “scatter plot” tab, the X-/Y-axis can be fully customized, while quick access for existing dimension reduction results will also be listed. “Fully customized” means an axis can be a dimension of a dimension reduction, the expression of a feature from an assay, or one of the cell annotations. In “bar plot” and “violin plot” tab, the X-axis is limited to cell annotation level, while the Y-axis can still be fully customized.
The color setting determines the color of each dot or bar in the plot. In “Scatter Plot” tab, colors can be set by the value of a dimension from a dimension reduction embedding, the expression value of a gene from an assay, one of the cell annotation, or a single color for all dots (cells). While SCTK only supports single color plotting for bar plot and violin plot.