pl_tracksplot
Generate compact gene expression plots for single-cell RNA sequencing data. Customize visualizations with color maps, group annotations, dendrograms, and logarithmic scaling to analyze and interpret gene activity patterns.
Instructions
tracksplot,compact plot of expression of a list of genes..
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| color_map | No | Color map to use for continuous variables. | |
| dendrogram | No | If True or a valid dendrogram key, a dendrogram based on the hierarchical clustering between the groupby categories is added. | |
| figsize | No | Figure size. Format is (width, height). | |
| gene_symbols | No | Column name in .var DataFrame that stores gene symbols. | |
| groupby | Yes | The key of the observation grouping to consider. | |
| 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 |
| log | No | Plot on logarithmic axis. | |
| palette | No | Colors to use for plotting categorical annotation groups. | |
| use_raw | No | Use raw attribute of adata if present. | |
| var_group_labels | No | Labels for each of the var_group_positions that want to be highlighted. | |
| var_group_positions | No | Use this parameter to highlight groups of var_names with brackets or color blocks between the given start and end positions. | |
| var_names | No | var_names should be a valid subset of adata.var_names or a mapping where the key is used as label to group the values. | |
| 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. |