pl_embedding
Generate scatter plots for user-specified embedding basis (e.g., UMAP, t-SNE) to visualize single-cell RNA sequencing data, with customizable parameters for color, size, and annotation.
Instructions
Scatter plot for user specified embedding basis (e.g. umap, tsne, etc).
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| add_outline | No | Add outline to scatter plot points. | |
| arrows | No | Show arrows. | |
| arrows_kwds | No | Passed to matplotlib's quiver function for drawing arrows. | |
| basis | Yes | Name of the obsm basis to use. | |
| cmap | No | Color map to use for continuous variables. Overrides color_map. | |
| color | No | Keys for annotations of observations/cells or variables/genes. | |
| color_map | No | Color map to use for continuous variables. | |
| colorbar_loc | No | Location of the colorbar. | right |
| components | No | For instance, ['1,2', '2,3']. To plot all available components use components='all'. | |
| dimensions | No | 0-indexed dimensions of the embedding to plot as integers. E.g. [(0, 1), (1, 2)]. | |
| edges | No | Show edges between nodes. | |
| edges_color | No | Color of edges. | grey |
| edges_width | No | Width of edges. | |
| figsize | No | Figure size. Format is (width, height). | |
| frameon | No | Draw a frame around the scatter plot. | |
| gene_symbols | No | Column name in .var DataFrame that stores gene symbols. | |
| groups | No | Restrict to a few categories in categorical observation annotation. | |
| hspace | No | Height space between panels. | |
| layer | No | Name of the AnnData object layer that wants to be plotted. | |
| legend_fontoutline | No | Line width of the legend font outline in pt. | |
| legend_fontsize | No | Numeric size in pt or string describing the size. | |
| legend_fontweight | No | Legend font weight. A numeric value in range 0-1000 or a string. | bold |
| legend_loc | No | Location of legend, either 'on data', 'right margin' or a valid keyword for the loc parameter. | right margin |
| marker | No | Matplotlib marker style for points. | . |
| mask_obs | No | A boolean array or a string mask expression to subset observations. | |
| na_color | No | Color to use for null or masked values. | lightgray |
| na_in_legend | No | Whether to include null values in the legend. | |
| ncols | No | Number of columns for multiple plots. | |
| neighbors_key | No | Where to look for neighbors connectivities. | |
| outline_color | No | Color of the outline for highlighted points. | |
| outline_width | No | Width of the outline for highlighted points. | |
| palette | No | Colors to use for plotting categorical annotation groups. | |
| projection | No | Projection of plot. | 2d |
| scale_factor | No | Scale factor for the plot. | |
| size | No | Point size. If None, is automatically computed. | |
| sort_order | No | For continuous annotations used as color parameter, plot data points with higher values on top of others. | |
| title | No | Title for the plot. | |
| use_raw | No | Use .raw attribute of adata for coloring with gene expression. | |
| vcenter | No | The value representing the center of the color scale. | |
| vmax | No | The value representing the upper limit of the color scale. | |
| vmin | No | The value representing the lower limit of the color scale. | |
| wspace | No | Width space between panels. |