"""
Plot graph structures
---------------------
This functions show how to plot graph structures, such as the transition matrix.
"""
import cellrank as cr
import numpy as np
adata = cr.datasets.pancreas_preprocessed("../example.h5ad")
adata
# %%
# First, we create a forward transition matrix using the high-level pipeline.
cr.tl.transition_matrix(
adata, show_progress_bar=False, weight_connectivities=0.2, softmax_scale=4
)
# %%
# We can now plot the transition matrix. Below we don't show any arrows, which dramatically speeds up the plotting.
cr.pl.graph(
adata,
"T_fwd",
edge_alpha=0.1,
node_size=5,
arrows=False,
keys="clusters",
keylocs="obs",
)
# %%
# To further illustrate the functionalities, let us only consider the `'Delta`' cluster. We can also filter the edges
# by their weights, as shown below. Only transitions with probability at least 0.1 are plotted.
ixs = np.where(adata.obs["clusters"] == "Delta")[0]
cr.pl.graph(adata, "T_fwd", ixs=ixs, arrows=True, node_size=200, filter_edges=(0.1, 1))
# %%
# Lastly, we can visualize different edge aggregations, such as minimum or maximum. Here we take at most 3 outgoing
# edges restricted to ``ixs`` for each node in descending order and color the nodes by the maximum outgoing weights.
# Aggregated values are always computed before any filtering happens, such as shown above.
#
# Here we also specify ``edge_reductions_restrict_to_ixs`` (by default, it is the same as ``ixs``) that computes the
# statistic between the cells marked with ``ixs`` and ``edge_reductions_restrict_to_ixs``.
#
# Below we compare the maximum transition from each of the `"Delta"` cells to any of the `"Beta"` cells.
cr.pl.graph(
adata,
"T_fwd",
ixs=ixs,
edge_alpha=0.5,
node_size=200,
keys="outgoing",
arrows=False,
top_n_edges=(3, False, "outgoing"),
title="outgoing to Beta",
edge_reductions=np.max,
edge_reductions_restrict_to_ixs=np.where(adata.obs["clusters"] == "Beta")[0],
)