How to use the scvelo.plotting.docs.doc_params function in scvelo

To help you get started, we’ve selected a few scvelo examples, based on popular ways it is used in public projects.

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github theislab / scvelo / scvelo / plotting / paga.py View on Github external
@doc_params(scatter=doc_scatter)
def paga(
    adata,
    basis=None,
    vkey="velocity",
    color=None,
    layer=None,
    title=None,
    threshold=None,
    layout=None,
    layout_kwds=None,
    init_pos=None,
    root=0,
    labels=None,
    single_component=False,
    dashed_edges="connectivities",
    solid_edges="transitions_confidence",
github theislab / scvelo / scvelo / plotting / scatter.py View on Github external
@doc_params(scatter=doc_scatter)
def tsne(adata, **kwargs):
    """\
    Scatter plot in tsne basis.
    Parameters
    ----------
    {scatter}

    Returns
    -------
    If `show==False` a :class:`~matplotlib.axes.Axes` or a list of it.
    """
    return scatter(adata, basis="tsne", **kwargs)
github theislab / scvelo / scvelo / plotting / scatter.py View on Github external
@doc_params(scatter=doc_scatter)
def pca(adata, **kwargs):
    """\
    Scatter plot in pca basis.
    Parameters
    ----------
    {scatter}

    Returns
    -------
    If `show==False` a :class:`~matplotlib.axes.Axes` or a list of it.
    """
    return scatter(adata, basis="pca", **kwargs)
github theislab / scvelo / scvelo / plotting / scatter.py View on Github external
@doc_params(scatter=doc_scatter)
def phate(adata, **kwargs):
    """\
    Scatter plot in phate basis.
    Parameters
    ----------
    {scatter}

    Returns
    -------
    If `show==False` a :class:`~matplotlib.axes.Axes` or a list of it.
    """
    return scatter(adata, basis="phate", **kwargs)
github theislab / scvelo / scvelo / plotting / velocity_embedding.py View on Github external
@doc_params(scatter=doc_scatter)
def velocity_embedding(
    adata,
    basis=None,
    vkey="velocity",
    density=None,
    arrow_size=None,
    arrow_length=None,
    scale=None,
    X=None,
    V=None,
    recompute=None,
    color=None,
    use_raw=None,
    layer=None,
    color_map=None,
    colorbar=True,
github theislab / scvelo / scvelo / plotting / velocity_embedding_grid.py View on Github external
@doc_params(scatter=doc_scatter)
def velocity_embedding_grid(
    adata,
    basis=None,
    vkey="velocity",
    density=None,
    smooth=None,
    min_mass=None,
    arrow_size=None,
    arrow_length=None,
    arrow_color=None,
    scale=None,
    autoscale=True,
    n_neighbors=None,
    recompute=None,
    X=None,
    V=None,
github theislab / scvelo / scvelo / plotting / scatter.py View on Github external
@doc_params(scatter=doc_scatter)
def umap(adata, **kwargs):
    """\
    Scatter plot in UMAP basis.
    Parameters
    ----------
    {scatter}

    Returns
    -------
    If `show==False` a :class:`~matplotlib.axes.Axes` or a list of it.
    """
    return scatter(adata, basis="umap", **kwargs)
github theislab / scvelo / scvelo / plotting / scatter.py View on Github external
@doc_params(scatter=doc_scatter)
def draw_graph(adata, layout=None, **kwargs):
    """\
    Scatter plot in draw_graph basis.
    Parameters
    ----------
    {scatter}

    Returns
    -------
    If `show==False` a :class:`~matplotlib.axes.Axes` or a list of it.
    """
    if layout is None:
        layout = f"{adata.uns['draw_graph']['params']['layout']}"
    basis = f"draw_graph_{layout}"
    if f"X_{basis}" not in adata.obsm_keys():
        raise ValueError(f"Could not find draw_graph_{layout} in adata.obs.")
github theislab / scvelo / scvelo / plotting / scatter.py View on Github external
@doc_params(scatter=doc_scatter)
def trimap(adata, **kwargs):
    """\
    Scatter plot in trimap basis.
    Parameters
    ----------
    {scatter}

    Returns
    -------
    If `show==False` a :class:`~matplotlib.axes.Axes` or a list of it.
    """
    return scatter(adata, basis="trimap", **kwargs)
github theislab / scvelo / scvelo / plotting / velocity_embedding_stream.py View on Github external
@doc_params(scatter=doc_scatter)
def velocity_embedding_stream(
    adata,
    basis=None,
    vkey="velocity",
    density=None,
    smooth=None,
    min_mass=None,
    cutoff_perc=None,
    arrow_color=None,
    linewidth=None,
    n_neighbors=None,
    recompute=None,
    color=None,
    use_raw=None,
    layer=None,
    color_map=None,