Skip to content

Expose random_state in tl.draw_graph #681

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
jpintar wants to merge 2 commits into
base: main
Choose a base branch
from
+15 −4
Open

Expose random_state in tl.draw_graph #681

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
ecd501c
Expose `random_state` in `tl.draw_graph`
jpintar May 30, 2026
2a47018
Release note edit
jpintar May 30, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions docs/release-notes/0.15.2.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
```
* Add `ptg.GuideAssignment.assign_mixture_model` for crispat-style Poisson-Gaussian guide assignment. The CUDA/nanobind implementation writes pertpy-compatible labels to `adata.obs` and stores both pertpy-style and crispat-style model readouts in `adata.var` {pr}`637` {smaller}`S Dicks`
* Add pseudobulk based distance metrics to {class}`~rapids_singlecell.ptg.Distance`: ``euclidean``, ``root_mean_squared_error``, ``mse``, ``mean_absolute_error``, ``pearson_distance``, ``cosine_distance``, ``r2_distance``. Matches ``pertpy.tl.Distance`` {pr}`676` {smaller}`S Dicks`
* ``tl.draw_graph`` now exposes the ``random_state`` parameter of ``cugraph.layout.force_atlas2`` {pr}`681` {smaller}`J Pintar`

```{rubric} Bug fixes
```
Expand Down
18 changes: 14 additions & 4 deletions src/rapids_singlecell/tools/_draw_graph.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,11 @@


def draw_graph(
adata: AnnData, *, init_pos: str | bool | None = None, max_iter: int = 500
adata: AnnData,
*,
init_pos: str | bool | None = None,
max_iter: int = 500,
random_state: int | None = 0,
) -> None:
"""
Force-directed graph drawing :cite:p:`Fruchterman1991,Jacomy2014`.
Expand All @@ -41,6 +45,10 @@ def draw_graph(
No error occurs when the algorithm terminates in this manner.
Good short-term quality can be achieved with 50-100 iterations.
Above 1000 iterations is discouraged.
random_state
Random state to use when initializing layout and generating
samples. Defaults to 0. If `None` is passed, a hash of process id,
time, and hostname is used by `cugraph`.

Returns
-------
Expand All @@ -59,9 +67,11 @@ def draw_graph(
case str() if init_pos in adata.obsm:
init_coords = adata.obsm[init_pos]
case str() if init_pos == "paga":
if random_state is None:
random_state = np.random.default_rng()
init_coords = get_init_pos_from_paga(
adata,
**_random_state_kwargs(get_init_pos_from_paga, 0),
**_random_state_kwargs(get_init_pos_from_paga, random_state),
neighbors_key="connectivities",
)
case _:
Expand Down Expand Up @@ -95,12 +105,12 @@ def draw_graph(
scaling_ratio=2.0,
strong_gravity_mode=False,
gravity=1.0,
random_state=0,
random_state=random_state,
)
positions = positions.sort_values("vertex").reset_index(drop=True)
positions = cp.vstack((positions["x"].to_cupy(), positions["y"].to_cupy())).T
layout = "fa"
adata.uns["draw_graph"] = {}
adata.uns["draw_graph"]["params"] = {"layout": layout, "random_state": 0}
adata.uns["draw_graph"]["params"] = {"layout": layout, "random_state": random_state}
key_added = f"X_draw_graph_{layout}"
adata.obsm[key_added] = positions.get() # Format output
Loading