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

# paste the error output here, if applicable
AttributeError                            Traceback (most recent call last)
<ipython-input-36-de7cf880ac12> in <module>
      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.