Rasterisation/vector_friendly not always working

[Hrovatin]

• [x] I have checked that this issue has not already been reported.
• [ ] I have confirmed this bug exists on the latest version of scanpy.
• [ ] (optional) I have confirmed this bug exists on the master branch of scanpy.

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I tried setting sc._settings.settings._vector_friendly=True This rasterises some of my figures, but not as expected.

UMAPs: Rasterized when saved, but if I save figures they are no longer rasterized in the notebook when shown (leading to large notebook). If I do not save the figure then the notebook stays small. Scatterplots: Not saved rasterized. Not sure about the notebook.

Maybe someone should also check other plots, such as violinplots with stripplots.

[RachellyN]

I also found out that vector_friendly works for sc.pl.umap but not for sc.pl.scatterplot

Here is a small piece of code to demonstrate it:

sc.set_figure_params(vector_friendly=True, dpi_save=300)  # Makes PDFs of scatter plots much smaller in size but still high-quality
clusters = data.obs[leiden_col].cat.categories
    for clust in range(0, len(clusters)):
        clust_name = clusters[clust]
        sc.pl.scatter(data, color=leiden_col, basis="umap", palette=["red"], groups=str(clust_name), size=7, show=False, ax=ax[clust], legend_loc="none", title=leiden_col) # won't be vector friendly
        sc.pl.umap(data, color=leiden_col,palette=["red"], groups=str(clust_name), size=7, show=False,ax=ax[clust], legend_loc="none") # will be vector friendly

plt.show()

[QqQss]

I found the same problem using scanpy.pl.violin. And did you guys find the solution?

[VPetukhov]

I found the same problem using scanpy.pl.violin.

It looks like the problem is in sns.violinplot, which ignores kwargs, so it's impossible to make it rasterized.