How to change the axis limits in scanpy for violin plots

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1

How do you change the axis limits in ScanPy for violin plots? Is this possible?

specifically for this type of plot

sc.pl.violin(adata, keys='total_counts', groupby='leiden',  xlabel="leiden cluster number", save="_leiden_clusters_total_counts")
2

Hi! You can get back the Axes object and manipulate e.g. the y-axis limits like so:

ax = sc.pl.violin(adata, keys='total_counts', groupby='leiden',  xlabel="leiden cluster number", show=False)
ax.set_ylim(bottom=0,top=100)

Of course don’t forget to save the plot afterwards, as now this will not happen automatically.

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