How to get the clade no.s after generating trajectory plot

[rialc13]

Hi. I am running the below code for creating trajectories -

st.spatial.trajectory.pseudotimespace_global(bdata,use_label="seurat_clusters",list_clusters=["4","13"])
st.pl.cluster_plot(bdata,use_label="seurat_clusters",show_trajectories=True,list_clusters=["4","13"],show_subcluster=True)

tree_plot(bdata, use_label="seurat_clusters")

After I generate the tree plot, I get the clade number information. Can you tell me how to fetch the number of clades & the clade number from my anndata object itself? For eg, if my iroot = cluster 0, & my list_clusters = 4,13, what will be the command for fetching the clade information just for this trajectory?

[duypham2108]

The name of the clade will be the starting (after pseudoroot) node. Currently, we don't have any function to extract it automatically. You can manually extract them by every sub-clusters from "sub_cluster_labels" in .obs. For example adata.obs[adata.obs.sub_cluster_labels.isin(["3","1"]) in your case

[rialc13]

Is there anyway we can get the clade information before generating the plot? For example, if I just run the function st.spatial.trajectory.pseudotimespace_global (not the st.pl.cluster_plot), how can I fetch the clade number?

[duypham2108]

You can extract the graph like this

import networkx as nx
from stlearn.utils import _read_graph
G = _read_graph(data,"PTS_graph")
G.remove_node(9999)
nx.draw_networkx(G)