No arrows displayed when running the Spatial trajectory inference analysis #317
Description
st.spatial.trajectory.pseudotimespace_global and using st.pl.cluster_plot to visualize the trajectories.
Description: I followed the tutorial and successfully completed the following steps:
Ran PCA on the data:
st.em.run_pca(data, n_comps=900, random_state=0)
Tiled the image:
st.pp.tiling(data, out_path="tiling", crop_size=40)
Used deep learning to extract features:
st.pp.extract_feature(data)
Applied the spatial-PCA adjustment using stSME:
st.spatial.morphology.adjust(data, use_data="X_pca", radius=200, method="median")
Calculated neighbors:
st.pp.neighbors(data, n_neighbors=15, use_rep='X_pca_morphology', random_state=0)
Performed Louvain clustering:
st.tl.clustering.louvain(data, random_state=0)
Afterward, I ran the following for trajectory inference:
data.uns["iroot"] = st.spatial.trajectory.set_root(data, use_label="louvain", cluster=4, use_raw=True)
st.spatial.trajectory.pseudotime(data, eps=101, use_rep="X_pca", use_label="louvain")
The output showed that available trajectory paths are stored in adata.uns['available_paths']:
{0: [4, 3], 1: [4, 3, 2], 3: [4, 2, 1], 2: [4, 3, 0], 5: [4, 3, 1]}
Then, I ran the global pseudotime-space trajectory method:
st.spatial.trajectory.pseudotimespace_global(data, use_label="louvain", list_clusters=["4", "2"])
Output: Start to construct the trajectory: 4 -> 2
Finally, I attempted to visualize the trajectory using st.pl.cluster_plot:
st.pl.cluster_plot(data, use_label="louvain", show_trajectories=True, list_clusters=["4", "2"],
show_subcluster=True, trajectory_edge_color="black", trajectory_arrowsize=12,
trajectory_width=12, size=20)
The plot shows the clusters and subclusters, but there are no arrows indicating the trajectory from cluster 4 to cluster 2. As a troubleshooting step, I increased the arrow width to 1000, and I could see some black area emerging from the corner of the plot, but still no clear arrows.
What I’ve tried:
Increased the arrow width to a large value, but it only produced a black patch in the corner of the plot.
Ensured that adata.uns['available_paths'] contains the expected trajectory paths.
Can someone help me understand why the arrows aren’t showing up in the plot? What other steps can I take to debug this?