How can I delete or rotate the legend of `sc.pl.stacked_violin`?

[danli349]

Hello:

How can I delete or rotate or change the position of the legend of sc.pl.stacked_violin?

Thanks

[flying-sheep]

We have plot classes that are used for all plots. The stacked_violin function is not more than:

https://github.com/scverse/scanpy/blob/ed3b277b2f498e3cab04c9416aaddf97eec8c3e2/scanpy/plotting/_stacked_violin.py#L679-L723

And the colorbar plotting is defined here:

https://github.com/scverse/scanpy/blob/ed3b277b2f498e3cab04c9416aaddf97eec8c3e2/scanpy/plotting/_baseplot_class.py#L493-L520

So currently, you’d have to do something like this, but I agree, this should be easier

from matplotlib import colormaps
from matplotlib.colorbar import Colorbar
from matplotlib.cm import ScalarMappable

class MyStackedViolin(StackedViolin):
     def _plot_colorbar(self, color_legend_ax, normalize):
         mappable = ScalarMappable(norm=normalize, cmap=colormaps[self.cmap])
         Colorbar(color_legend_ax, mappable=mappable, orientation='vertical')

vp = StackedViolin(adata, var_names, ...)
vp.make_figure()

[danli349]

@flying-sheep Thanks for helping!
I tried your code, but it does not work as expected.

class MyStackedViolin(sc.pl.StackedViolin):
     def _plot_colorbar(self, color_legend_ax, normalize):
         mappable = ScalarMappable(norm=normalize, cmap=colormaps[self.cmap])
         Colorbar(color_legend_ax, mappable=mappable, orientation='vertical')

vp = MyStackedViolin(adata_luminals, L1_signature,
                    groupby='leiden_r1',
                    cmap='coolwarm',
                    swap_axes = True)
vp.make_figure()

[flying-sheep]

I see, there’s also code to make that exact shape. Seems like you need to override this as well:

https://github.com/scverse/scanpy/blob/ed3b277b2f498e3cab04c9416aaddf97eec8c3e2/scanpy/plotting/_baseplot_class.py#L522-L542

maybe simply

 def _plot_legend(self, legend_ax, return_ax_dict, normalize):  
     self._plot_colorbar(legend_ax, normalize) 
     return_ax_dict['color_legend_ax'] = color_legend_ax

but as said: we will start working on a more flexible and less fiddle plotting API

[danli349]

@flying-sheep Thanks! Now it works better, but the size is out of control.

When I combine several plots together using plt.subplots

from matplotlib.pyplot import rc_context
with rc_context({'figure.figsize': (3, 3)}):
    fig, ax = plt.subplots(1, 4, figsize=(12,4))
    ax[0] = sc.pl.stacked_violin(adata_luminals[adata_luminals.obs['sample'] == adata_luminals.obs['sample'].cat.categories[0]], 
                                  var_names = gene, use_raw = True, ax=ax[0],
                                  groupby='leiden_r1', 
                                  cmap='coolwarm', dendrogram=False,
                                  swap_axes = True, stripplot = False,
                                  title = adata_luminals.obs['sample'].cat.categories[0], show=False)
    ax[1] = sc.pl.stacked_violin(adata_luminals[adata_luminals.obs['sample'] == adata_luminals.obs['sample'].cat.categories[1]], 
                                  var_names = gene, use_raw = True, ax=ax[1],
                                  groupby='leiden_r1', 
                                  cmap='coolwarm', dendrogram=False,
                                  swap_axes = True, stripplot = False,
                                  title = adata_luminals.obs['sample'].cat.categories[1], show=False)
    ax[2] = sc.pl.stacked_violin(adata_luminals[adata_luminals.obs['sample'] == adata_luminals.obs['sample'].cat.categories[2]], 
                                  var_names = gene, use_raw = True, ax=ax[2],
                                  groupby='leiden_r1', 
                                  cmap='coolwarm', dendrogram=False,
                                  swap_axes = True, stripplot = False,
                                  title = adata_luminals.obs['sample'].cat.categories[2], show=False)
    ax[3] = sc.pl.stacked_violin(adata_luminals[adata_luminals.obs['sample'] == adata_luminals.obs['sample'].cat.categories[3]], 
                                  var_names = gene, use_raw = True, ax=ax[3],
                                  groupby='leiden_r1', 
                                  cmap='coolwarm', dendrogram=False,
                                  swap_axes = True, stripplot = False,
                                  title = adata_luminals.obs['sample'].cat.categories[3], show=False)
#fig.delaxes(fig.axes[11])
#fig.delaxes(fig.axes[18])
#fig.delaxes(fig.axes[25])
#fig.delaxes(fig.axes[32])
plt.draw()

I would like to omit the color bars in the middle and only keep the last one. Could you please show me how to delete it? Thanks

[flying-sheep]

That should be simply groupby='sample' instead of multiple plot calls.

[danli349]

Yes I would like to separate both sample and leiden_r1, I should create a new variable adata.obs['leiden+sample'].

[flying-sheep]

you can just do groupby=['leiden_r1', 'sample']

[janschleicher]

Are there any updates on this? I am facing the same issues with scanpy.pl.matrixplot. It would be great if one could pass arguments to the colorbar plotting (such as orientation, ticks, aspect, etc.). It would also be helpful to return the colorbar as part of the dictionary that is returned with show=False to be able to modify it after plot creation. If I am not mistaken, the colorbar itself is currently not accessible from the axes_dict["color_legend_ax"]. Thanks for your response.