pl_scatter
Generate scatter plots to visualize relationships between two variables in single-cell RNA sequencing data. Customize plots with color maps, annotations, and layout adjustments for clear data insights.
Instructions
Plot a scatter plot of two variables, Scatter plot along observations or variables axes.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| alpha | No | Alpha value for the plot. | |
| basis | No | Basis to use for embedding. | |
| color | No | Keys for annotations of observations/cells or variables/genes, or a hex color specification. | |
| color_map | No | Color map to use for continuous variables. | |
| components | No | For instance, ['1,2', '2,3']. To plot all available components use components='all'. | |
| figsize | No | Figure size. Format is (width, height). | |
| groups | No | Restrict to a few categories in categorical observation annotation. | |
| layers | No | Use the layers attribute of adata if present: specify the layer for x, y and color. | |
| left_margin | No | Adjust the width of the left margin. | |
| 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 |
| palette | No | Colors to use for plotting categorical annotation groups. | |
| projection | No | Projection of plot. | 2d |
| right_margin | No | Adjust the width of the right margin. | |
| sort_order | No | For continuous annotations used as color parameter, plot data points with higher values on top of others. | |
| use_raw | No | Whether to use raw attribute of adata. Defaults to True if .raw is present. | |
| 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. | |
| x | No | x coordinate. | |
| y | No | y coordinate. |