Issues with sc.pl.pca when using components

I try to use sc.pl.pca selecting components. According to the documentation the following should work:

import scanpy.api as sc
sc.logging.print_versions()
adata = sc.datasets.blobs()
sc.tl.pca(adata)
sc.pl.pca(adata, components=['1,2', '2,3'])

However, I get an error. The output of the code above is:

scanpy==0+unknown anndata==0.6.9 numpy==1.14.5 scipy==1.1.0 pandas==0.23.4 scikit-learn==0.19.1 statsmodels==0.9.0 python-igraph==0.7.1 louvain==0.6.1 
... storing 'blobs' as categorical

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-16-4cd21e9edf25> in <module>()
      3 adata = sc.datasets.blobs()
      4 sc.tl.pca(adata)
----> 5 sc.pl.pca(adata, components=['1,2', '2,3'])

~/software/scanpy/scanpy/plotting/tools/__init__.py in pca(adata, color, use_raw, sort_order, alpha, groups, components, projection, legend_loc, legend_fontsize, legend_fontweight, color_map, palette, right_margin, size, title, show, save, ax)
    114         title=title,
    115         show=False,
--> 116         save=False, ax=ax)
    117     utils.savefig_or_show('pca_scatter', show=show, save=save)
    118     if show == False: return axs

~/software/scanpy/scanpy/plotting/anndata.py in scatter(adata, x, y, color, use_raw, layers, sort_order, alpha, basis, groups, components, projection, legend_loc, legend_fontsize, legend_fontweight, color_map, palette, frameon, right_margin, left_margin, size, title, show, save, ax)
    110             show=show,
    111             save=save,
--> 112             ax=ax)
    113     elif x is not None and y is not None:
    114         if ((x in adata.obs.keys() or x in adata.var.index)

~/software/scanpy/scanpy/plotting/anndata.py in _scatter_obs(adata, x, y, color, use_raw, layers, sort_order, alpha, basis, groups, components, projection, legend_loc, legend_fontsize, legend_fontweight, color_map, palette, frameon, right_margin, left_margin, size, title, show, save, ax)
    291     if components is None: components = '1,2' if '2d' in projection else '1,2,3'
    292     if isinstance(components, str): components = components.split(',')
--> 293     components = np.array(components).astype(int) - 1
    294     keys = ['grey'] if color is None else [color] if isinstance(color, str) else color
    295     if title is not None and isinstance(title, str):

ValueError: invalid literal for int() with base 10: '1,2'

[fbnrst]

@LuckyMD, thanks for the workaround which indeed helps for now.

[falexwolf]

Hey @LuckyMD, @fidelram is currently completely rewriting the whole scatter plotting module. So let’s not address this in the current code. But, yes in principle, we should add it so that diffmap and pca behave consistently.