Open adkinsrs opened 2 days ago
Output when using a list of marker genes in the var_names
arg
Output when using a dict of marker genes in the var_names
arg
Yeah, that’s true.
I think depending on what’s happening, it’s actually the spacer we add, not the area for the dendrogram, but sometimes we also need that spacer …
Our plotting code is complicated and needs to be overhauled. If anyone feels like diving int
I was able to "hack" my way to a solution. However I needed to call StackedViolin.make_figure
to actually generate the figure that I could remove Axes from, and this creates the issue of showing the plot twice (one incorrect, one correct) in a Jupyter notebook. In a script though this shouldn't be an issue though.
marker_genes = ["Pou4f3", "Calb2", "Pvalb", "Smpx", "Mlf1", "Sox2"] # 5 random Cochlear HCs P7 + Sox2
violin_fig = sc.pl.stacked_violin(vis_adata, marker_genes, var_group_positions=None, title="Marker gene expression per cluster", groupby="spatial_clusters", cmap="YlOrRd", show=False, return_fig=True)
# Remove the existing legend and add a new vertically-oriented one
violin_fig.legend(show = False)
violin_fig.add_totals()
violin_fig.make_figure()
# For some reason, deleting all axes and remaking the figure makes it without the spacer above the plot (which was in ax[2] I think)
violin_axes = violin_fig.fig.get_axes()
for ax in violin_axes:
violin_fig.fig.delaxes(ax)
violin_fig.make_figure()
very cool! Happy you found a workaround. I’d really like to toss a lot of the plotting out and replace it with something declarative …
Please make sure these conditions are met
What happened?
Basically I am creating a stacked violin plot that uses a list of marker genes for the "var_names" argument. But whenever I create the plot, it has extra whitespace at the top of the plot where the marker gene labels should go. This is very evident when you add a figure title, which gets place above the padding whitespace. I have not really found a way around this, and am currently looking through the scanpy internal code to see if there is some padding setting that I can undo. If there is a workaround to this or some option that I am missing I would like to know.
Thanks!
Minimal code sample
Error output
Will post in the next comment on this thread. Seems I cannot drag-n-drop images into this block.
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