`scv.pl.velocity_embedding_stream` does not work with `right_margin` specified

[seigfried]

Hi could you please help? I tried to make a velocity_embedding_stream plot and the dots get cut on all four sides. I will try to list down the issues I faced Issue 1 : Dots getting truncated on all four sides  Issue 2 : Since dots were truncated, I thought that increasing the margins would help. I tried `?scv.pl.velocity_embedding_stream` and I saw the functions `left_margin` and `right_margin`. However, when I tried using either of them, I got an error. ...

# paste your code here, if applicable
import scvelo as scv
import pandas as pd
import matplotlib as mpl
import loompy

adata = scv.read("velocity.loom", cache=True)
adata.var_names_make_unique
adata2 = scv.read("scRNAseq.h5ad")

adata3 = scv.utils.merge(adata,adata2)
scv.pp.filter_and_normalize(adata3, min_shared_counts=20, n_top_genes=2000)
scv.pp.moments(adata3, n_pcs=30, n_neighbors=30)
scv.tl.velocity(adata3)
scv.tl.velocity_graph(adata3)

import matplotlib.pyplot as plt
plt.rcParams.update({'lines.markersize' : '15'})

# Snippet for Issue 1
scv.pl.velocity_embedding_stream(adata3, color_map=mpl.cm.Reds, legend_loc="right",
                                 color="leiden", basis='umap', fontsize=20, dpi=300, figsize=[8,8])

# Snippet for Issue 2
scv.pl.velocity_embedding_stream(adata3, color_map=mpl.cm.Reds, legend_loc="right",
                                 right_margin=0.2, color="leiden", basis='umap', fontsize=20, dpi=300, figsize=[8,8])

Error output

```pytb # paste the error output here, if applicable AttributeError Traceback (most recent call last) in 2 plt.rcParams.update({'lines.markersize' : '15'}) 3 ----> 4 scv.pl.velocity_embedding_stream(adata3, color_map=mpl.cm.Reds, legend_loc="right", 5 right_margin=0.2, color="Specific_CellType", basis='umap', fontsize=20, dpi=300, figsize=[8,8]) 6 #scv.pl.velocity_embedding_stream(adata3, color_map=mpl.cm.Reds, color="leiden", basis='umap', ~\Anaconda3\envs\Velocyto\lib\site-packages\scvelo\plotting\velocity_embedding_stream.py in velocity_embedding_stream(adata, basis, vkey, density, smooth, min_mass, cutoff_perc, arrow_color, linewidth, n_neighbors, recompute, color, use_raw, layer, color_map, colorbar, palette, size, alpha, perc, X, V, X_grid, V_grid, sort_order, groups, components, legend_loc, legend_fontsize, legend_fontweight, xlabel, ylabel, title, fontsize, figsize, dpi, frameon, show, save, ax, ncols, **kwargs) 214 215 size = 8 * default_size(adata) if size is None else size --> 216 ax = scatter( 217 adata, 218 layer=layer, ~\Anaconda3\envs\Velocyto\lib\site-packages\scvelo\plotting\scatter.py in scatter(adata, basis, x, y, vkey, color, use_raw, layer, color_map, colorbar, palette, size, alpha, linewidth, linecolor, perc, groups, sort_order, components, projection, legend_loc, legend_loc_lines, legend_fontsize, legend_fontweight, legend_fontoutline, xlabel, ylabel, title, fontsize, figsize, xlim, ylim, add_density, add_assignments, add_linfit, add_polyfit, add_rug, add_text, add_text_pos, add_outline, outline_width, outline_color, n_convolve, smooth, rescale_color, color_gradients, dpi, frameon, zorder, ncols, nrows, wspace, hspace, show, save, ax, **kwargs) 593 kwargs["s"] = np.array(kwargs["s"])[order] 594 --> 595 smp = ax.scatter( 596 x, y, c=c, alpha=alpha, marker=".", zorder=zorder, **kwargs 597 ) ~\Anaconda3\envs\Velocyto\lib\site-packages\matplotlib\__init__.py in inner(ax, data, *args, **kwargs) 1350 def inner(ax, *args, data=None, **kwargs): 1351 if data is None: -> 1352 return func(ax, *map(sanitize_sequence, args), **kwargs) 1353 1354 bound = new_sig.bind(ax, *args, **kwargs) ~\Anaconda3\envs\Velocyto\lib\site-packages\matplotlib\axes\_axes.py in scatter(self, x, y, s, c, marker, cmap, norm, vmin, vmax, alpha, linewidths, edgecolors, plotnonfinite, **kwargs) 4575 ) 4576 collection.set_transform(mtransforms.IdentityTransform()) -> 4577 collection.update(kwargs) 4578 4579 if colors is None: ~\Anaconda3\envs\Velocyto\lib\site-packages\matplotlib\artist.py in update(self, props) 1060 func = getattr(self, f"set_{k}", None) 1061 if not callable(func): -> 1062 raise AttributeError(f"{type(self).__name__!r} object " 1063 f"has no property {k!r}") 1064 ret.append(func(v)) AttributeError: 'PathCollection' object has no property 'right_margin' ```

Versions

``` # paste the ouput of scv.logging.print_versions() here scvelo==0.2.3 scanpy==1.7.2 anndata==0.7.6 loompy==3.0.6 numpy==1.20.3 scipy==1.6.3 matplotlib==3.4.1 sklearn==0.24.2 pandas==1.2.4 ```

[WeilerP]

@seigfried, two things:

1. Would please update to the latest package versions and check that the problem persists?
2. Could you please provide an exemplary code snippet I can simply copy and paste? (For example using the Pancreas dataset used in the scvelo paper.)

Using the pancreas dataset, I can reproduce the problem regarding right_margin but not the cutoff.

[WeilerP]

@seigfried, two things:

1. Would please update to the latest package versions and check that the problem persists?
2. Could you please provide an exemplary code snippet I can simply copy and paste? (For example using the Pancreas dataset used in the scvelo paper.)

Using the pancreas dataset, I can reproduce the problem regarding right_margin but not the cutoff.

@seigfried, nevermind, I managed to reproduce the cutoff problem. I'll open a separate issue, comment a bit more there and investigate it ASAP.