dynamo.pl.feature_genes
- dynamo.pl.feature_genes(adata, layer='X', mode=None, figsize=(4, 3), save_show_or_return='show', save_kwargs={})[source]
Plot selected feature genes on top of the mean vs. dispersion scatterplot.
- Parameters:
adata (
AnnData) – an AnnData object.layer (
str) – the data from a particular layer (include X) used for making the feature gene plot. Defaults to “X”.mode (
Optional[Literal['cv_dispersion','fano_dispersion','seurat_dispersion','gini']]) – the method to select the feature genes (can be either one kind of dispersion or gini). Defaults to None.figsize (
tuple) – the size of each panel of the figure. Defaults to (4, 3).save_show_or_return (
Literal['save','show','return']) – whether to save, show, or return the generated figure. Can be one of ‘save’, ‘show’, or ‘return’. Defaults to “show”.save_kwargs (
Dict[str,Any]) – a dictionary that will be passed to the save_show_ret function. By default, it is an empty dictionary and the save_show_ret function will use the {“path”: None, “prefix”: ‘feature_genes’, “dpi”: None, “ext”: ‘pdf’, “transparent”: True, “close”: True, “verbose”: True} as its parameters. Otherwise, you can provide a dictionary that properly modify those keys according to your needs. Defaults to {}.
- Raises:
ValueError – vector machine regression result not available in the AnnData object.
- Return type:
- Returns:
None would be returned by default. If save_show_or_return is set to be ‘return’, the PathCollection generated with pyplot.scatter would be returned.