-
Notifications
You must be signed in to change notification settings - Fork 101
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
5329105
commit ede811b
Showing
4 changed files
with
117 additions
and
8 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,8 @@ | ||
| from .scatter import scatter | ||
| from .velocity import velocity | ||
| from .velocity_embedding import velocity_embedding | ||
| from .velocity_embedding_grid import velocity_embedding_grid, velocity_embedding_stream | ||
| from .velocity_embedding_grid import velocity_embedding_grid | ||
| from .velocity_embedding_stream import velocity_embedding_stream | ||
| from .velocity_graph import velocity_graph | ||
| from .utils import hist | ||
| from scanpy.api.pl import paga, paga_compare, rank_genes_groups |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,108 @@ | ||
| from ..tools.velocity_embedding import velocity_embedding | ||
| from .utils import default_basis, default_size, get_components, savefig, make_unique_list | ||
| from .velocity_embedding_grid import compute_velocity_on_grid | ||
| from .scatter import scatter | ||
| from .docs import doc_scatter, doc_params | ||
|
|
||
| from matplotlib import rcParams | ||
| import matplotlib.pyplot as pl | ||
| import numpy as np | ||
|
|
||
|
|
||
| @doc_params(scatter=doc_scatter) | ||
| def velocity_embedding_stream(adata, basis=None, vkey='velocity', density=None, smooth=None, linewidth=None, | ||
| n_neighbors=None, X=None, V=None, X_grid=None, V_grid=None, color=None, use_raw=None, | ||
| layer=None, color_map=None, colorbar=False, palette=None, size=None, alpha=.1, perc=None, | ||
| sort_order=True, groups=None, components=None, legend_loc='on data', | ||
| legend_fontsize=None, legend_fontweight=None, right_margin=None, left_margin=None, | ||
| xlabel=None, ylabel=None, title=None, fontsize=None, figsize=None, dpi=None, frameon=None, | ||
| show=True, save=None, ax=None, ncols=None, **kwargs): | ||
| """\ | ||
| Stream plot of velocities on the embedding. | ||
| Arguments | ||
| --------- | ||
| adata: :class:`~anndata.AnnData` | ||
| Annotated data matrix. | ||
| x: `str`, `np.ndarray` or `None` (default: `None`) | ||
| x coordinate | ||
| y: `str`, `np.ndarray` or `None` (default: `None`) | ||
| y coordinate | ||
| vkey: `str` or `None` (default: `None`) | ||
| Key for annotations of observations/cells or variables/genes. | ||
| density: `float` (default: 1) | ||
| Amount of velocities to show - 0 none to 1 all | ||
| smooth: `float` (default: 0.5) | ||
| Multiplication factor for scale in Gaussian kernel around grid point. | ||
| linewidth: `float` (default: 1) | ||
| Line width for streamplot. | ||
| n_neighbors: `int` (default: None) | ||
| Number of neighbors to consider around grid point. | ||
| X: `np.ndarray` (default: None) | ||
| Embedding grid point coordinates | ||
| V: `np.ndarray` (default: None) | ||
| Embedding grid velocity coordinates | ||
| {scatter} | ||
| Returns | ||
| ------- | ||
| `matplotlib.Axis` if `show==False` | ||
| """ | ||
| basis = default_basis(adata) if basis is None else basis | ||
| colors, layers, vkeys = make_unique_list(color, allow_array=True), make_unique_list(layer), make_unique_list(vkey) | ||
| for key in vkeys: | ||
| if key + '_' + basis not in adata.obsm_keys() and V is None: | ||
| velocity_embedding(adata, basis=basis, vkey=key) | ||
| color, layer, vkey = colors[0], layers[0], vkeys[0] | ||
|
|
||
| if X_grid is None or V_grid is None: | ||
| X_emb = adata.obsm['X_' + basis][:, get_components(components, basis)] if X is None else X[:, :2] | ||
| V_emb = adata.obsm[vkey + '_' + basis][:, get_components(components, basis)] if V is None else V[:, :2] | ||
| X_grid, V_grid = compute_velocity_on_grid(X_emb=X_emb, V_emb=V_emb, density=1, smooth=smooth, | ||
| n_neighbors=n_neighbors, autoscale=False, adjust_for_stream=True) | ||
| lengths = np.sqrt((V_grid ** 2).sum(0)) | ||
| linewidth = 1 if linewidth is None else linewidth | ||
| linewidth *= 2 * lengths / lengths[~np.isnan(lengths)].max() | ||
|
|
||
| scatter_kwargs = {"basis": basis, "perc": perc, "use_raw": use_raw, "sort_order": sort_order, "alpha": alpha, | ||
| "components": components, "legend_loc": legend_loc, "groups": groups, | ||
| "legend_fontsize": legend_fontsize, "legend_fontweight": legend_fontweight, "palette": palette, | ||
| "color_map": color_map, "frameon": frameon, "title": title, "xlabel": xlabel, "ylabel": ylabel, | ||
| "right_margin": right_margin, "left_margin": left_margin, "colorbar": colorbar, "dpi": dpi, | ||
| "fontsize": fontsize, "show": False, "save": None} | ||
|
|
||
| multikey = colors if len(colors) > 1 else layers if len(layers) > 1 else vkeys if len(vkeys) > 1 else None | ||
| if multikey is not None: | ||
| ncols = len(multikey) if ncols is None else min(len(multikey), ncols) | ||
| nrows = int(np.ceil(len(multikey) / ncols)) | ||
| figsize = rcParams['figure.figsize'] if figsize is None else figsize | ||
| for i, gs in enumerate( | ||
| pl.GridSpec(nrows, ncols, pl.figure(None, (figsize[0] * ncols, figsize[1] * nrows), dpi=dpi))): | ||
| if i < len(multikey): | ||
| velocity_embedding_stream(adata, density=density, size=size, smooth=smooth, n_neighbors=n_neighbors, | ||
| linewidth=linewidth, ax=pl.subplot(gs), | ||
| color=colors[i] if len(colors) > 1 else color, | ||
| layer=layers[i] if len(layers) > 1 else layer, | ||
| vkey=vkeys[i] if len(vkeys) > 1 else vkey, | ||
| X_grid=None if len(vkeys) > 1 else X_grid, | ||
| V_grid=None if len(vkeys) > 1 else V_grid, **scatter_kwargs, **kwargs) | ||
| if isinstance(save, str): savefig('' if basis is None else basis, dpi=dpi, save=save, show=show) | ||
| if show: | ||
| pl.show() | ||
| else: | ||
| return ax | ||
|
|
||
| else: | ||
| ax = pl.figure(None, figsize, dpi=dpi).gca() if ax is None else ax | ||
|
|
||
| density = 1 if density is None else density | ||
| stream_kwargs = {"linewidth": linewidth, "density": 2 * density} | ||
| stream_kwargs.update(kwargs) | ||
| pl.streamplot(X_grid[0], X_grid[1], V_grid[0], V_grid[1], color='grey', zorder=3, **stream_kwargs) | ||
|
|
||
| size = 4 * default_size(adata) if size is None else size | ||
| ax = scatter(adata, layer=layer, color=color, size=size, ax=ax, zorder=0, **scatter_kwargs) | ||
|
|
||
| if isinstance(save, str): savefig('' if basis is None else basis, dpi=dpi, save=save, show=show) | ||
| if show: pl.show() | ||
| else: return ax |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters