phlower.pl.plot_density_grid
- phlower.pl.plot_density_grid(adata: AnnData, graph_name=None, layout_name=None, cluster_name='trajs_clusters', trajs_name='knn_trajs', retain_clusters=[], sample_n=10000, figsize=(20, 16), title_prefix='cluster_', bg_alpha=0.5, node_size=2, return_fig=False, **args)
plot density grid of clusters
Parameters
- adata: AnnData
an Annodata object
- graph_name: str
key of the graph in adata.uns, default is None
- layout_name: str
key of the layout in adata.obsm, default is None
- cluster_name: str
key of the cluster in adata.obs, default is ‘trajs_clusters’
- trajs_name: str
key of the trajs in adata.uns, default is ‘knn_trajs’
- retain_clusters: list
list of clusters to plot, default is [] to use all
- sample_n: int
number of cells to sample, default is 10000
- figsize: tuple
figure size, default is (20,16)
- title_prefix: str
prefix of the title, default is ‘cluster_’
- bg_alpha: float
background alpha, default is 0.5
- node_size: float
node size, default is 2
- return_fig: bool
whether to return the figure, default is False