How to use the scvelo.plotting.scatter.scatter function in scvelo

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github theislab / scvelo / scvelo / plotting / velocity_embedding_grid.py View on Github external
quiver_kwargs.update({arg: kwargs[arg]})
            else:
                scatter_kwargs.update({arg: kwargs[arg]})

        ax.quiver(
            X_grid[:, 0], X_grid[:, 1], V_grid[:, 0], V_grid[:, 1], **quiver_kwargs
        )

        if principal_curve:
            curve = adata.uns["principal_curve"]["projections"]
            pl.plot(curve[:, 0], curve[:, 1], c="w", lw=6, zorder=4)
            pl.plot(curve[:, 0], curve[:, 1], c="k", lw=3, zorder=5)

        size = 4 * default_size(adata) if size is None else size

        ax = scatter(
            adata,
            layer=layer,
            color=color,
            size=size,
            title=title,
            ax=ax,
            zorder=0,
            **scatter_kwargs,
        )

        savefig_or_show(dpi=dpi, save=save, show=show)
        if show is False:
            return ax
github theislab / scvelo / scvelo / plotting / paga.py View on Github external
kwargs["frameon"] = paga_kwargs["frameon"]
        if title is None:
            title = (
                f"paga ({paga_groups})"
                if transitions is None
                else f"paga velocity-graph ({paga_groups})"
            )
        paga_kwargs["title"] = title

        ax = pl.figure(None, figsize, dpi=dpi).gca() if ax is None else ax
        if scatter_flag and basis is not None:
            if "alpha" not in kwargs:
                kwargs["alpha"] = 0.5
            kwargs.update(dict(basis=basis, layer=layer, color=paga_groups, size=size))
            kwargs.update(dict(vkey=vkey, title=title, ax=ax, show=False, save=None))
            ax = scatter(adata, x=x, y=y, zorder=0, **kwargs)
        text_kwds = {"zorder": 1000, "alpha": legend_loc == "on data"}
        _paga(adata, ax=ax, show=False, text_kwds=text_kwds, **paga_kwargs)

        savefig_or_show(dpi=dpi, save=save, show=show)
        if show is False:
            return ax
github theislab / scvelo / scvelo / plotting / velocity_embedding.py View on Github external
quiver3d_kwargs = {"zorder": 3, "linewidth": 0.5, "arrow_length_ratio": 0.3}
            c = list(c) + [element for element in list(c) for _ in range(2)]
            if is_color_like(c[0]):
                ax.quiver(x0, x1, x2, v0, v1, v2, color=c, **quiver3d_kwargs)
            else:
                ax.quiver(x0, x1, x2, v0, v1, v2, c, **quiver3d_kwargs)
        else:
            quiver_kwargs.update({"zorder": 3})
            if is_color_like(c[0]):
                ax.quiver(X[:, 0], X[:, 1], V[:, 0], V[:, 1], color=c, **quiver_kwargs)
            else:
                ax.quiver(X[:, 0], X[:, 1], V[:, 0], V[:, 1], c, **quiver_kwargs)

        scatter_kwargs.update({"basis": basis, "x": x, "y": y, "color": color})
        scatter_kwargs.update({"vkey": vkey, "layer": layer})
        ax = scatter(adata, size=size, title=title, ax=ax, zorder=0, **scatter_kwargs)

        savefig_or_show(dpi=dpi, save=save, show=show)
        if show is False:
            return ax
github theislab / scvelo / scvelo / plotting / velocity_embedding_stream.py View on Github external
stream_kwargs = {
            "linewidth": linewidth,
            "density": 2 * density,
            "zorder": 3,
            "color": "k" if arrow_color is None else arrow_color,
        }
        for arg in list(kwargs):
            if arg in stream_kwargs:
                stream_kwargs.update({arg: kwargs[arg]})
            else:
                scatter_kwargs.update({arg: kwargs[arg]})

        ax.streamplot(X_grid[0], X_grid[1], V_grid[0], V_grid[1], **stream_kwargs)

        size = 8 * default_size(adata) if size is None else size
        ax = scatter(
            adata,
            layer=layer,
            color=color,
            size=size,
            title=title,
            ax=ax,
            zorder=0,
            **scatter_kwargs,
        )

        savefig_or_show(dpi=dpi, save=save, show=show)
        if show is False:
            return ax
github theislab / scvelo / scvelo / plotting / velocity.py View on Github external
if mode == "stochastic":
            ss, us = second_order_moments(_adata)
            s, u, ss, us = s.flatten(), u.flatten(), ss.flatten(), us.flatten()
            fit = stochastic_fits[0]

            ax = pl.subplot(gs[v * nplts + len(layers) + 1])
            beta, offset = 1, 0
            if f"{fit}_beta" in adata.var.keys():
                beta = _adata.var[f"{fit}_beta"]
            if f"{fit}_offset" in adata.var.keys():
                offset = _adata.var[f"{fit}_offset"]
            x = np.array(2 * (ss - s ** 2) - s)
            y = np.array(2 * (us - u * s) + u + 2 * s * offset / beta)
            kwargs["xlabel"] = r"2 $\Sigma_s - \langle s \rangle$"
            kwargs["ylabel"] = r"2 $\Sigma_{us} + \langle u \rangle$"
            scatter(
                adata,
                x=x,
                y=y,
                color=color,
                title=var,
                frameon=True,
                ax=ax,
                save=False,
                show=False,
                **scatter_kwargs,
                **kwargs,
            )

            xnew = np.linspace(np.min(x), np.max(x) * 1.02)
            for fit in stochastic_fits:
                gamma, beta, offset2 = 1, 1, 0
github theislab / scvelo / scvelo / plotting / paga.py View on Github external
)

    scatter_kwargs.update({"alpha": 0, "color": groups_key})
    x, y = pos[:, 0], pos[:, 1]

    if plot:
        axs_pars = setup_axes(ax=ax, panels=colors, colorbars=colorbars)
        axs, panel_pos, draw_region_width, _ = axs_pars

        if len(colors) == 1 and not isinstance(axs, list):
            axs = [axs]

        for icolor, c in enumerate(colors):
            if title[icolor] is not None:
                axs[icolor].set_title(title[icolor])
            axs[icolor] = scatter(
                adata,
                x=x,
                y=y,
                title=title[icolor],
                ax=axs[icolor],
                save=None,
                zorder=0,
                show=False,
                **scatter_kwargs,
            )
            sct = _paga_graph(
                adata,
                axs[icolor],
                colors=c,
                solid_edges=solid_edges,
                dashed_edges=dashed_edges,