sc.pl.rank_genes_groups_dotplot

[rojinsafavi]

I get the following error when I tun dotplot:

ValueError                                Traceback (most recent call last)
<ipython-input-54-afab88c299fa> in <module>()
----> 1 sc.pl.rank_genes_groups_dotplot(vitro,['MYL2'], groupby='louvain')

/projects/sysbio/projects/czi/immune/anaconda2/envs/py36/lib/python3.6/site-packages/scanpy/plotting/_tools/__init__.py in rank_genes_groups_dotplot(adata, groups, n_genes, groupby, key, show, save, **kwds)
    409 
    410     _rank_genes_groups_plot(adata, plot_type='dotplot', groups=groups, n_genes=n_genes,
--> 411                             groupby=groupby, key=key, show=show, save=save, **kwds)
    412 
    413 

/projects/sysbio/projects/czi/immune/anaconda2/envs/py36/lib/python3.6/site-packages/scanpy/plotting/_tools/__init__.py in _rank_genes_groups_plot(adata, plot_type, groups, n_genes, groupby, key, show, save, **kwds)
    291 
    292     # sum(list, []) is used to flatten the gene list
--> 293     gene_names = sum([list(adata.uns[key]['names'][x][:n_genes]) for x in group_names], [])
    294 
    295     if plot_type == 'dotplot':

/projects/sysbio/projects/czi/immune/anaconda2/envs/py36/lib/python3.6/site-packages/scanpy/plotting/_tools/__init__.py in <listcomp>(.0)
    291 
    292     # sum(list, []) is used to flatten the gene list
--> 293     gene_names = sum([list(adata.uns[key]['names'][x][:n_genes]) for x in group_names], [])
    294 
    295     if plot_type == 'dotplot':

ValueError: no field of name MYL2

Do we need to store marker genes within the adata object?

[fidelram]

Just delete MY2L, or use sc.pl.dotplot

…

On 25 Feb 2019, at 18:37, rojin ***@***.***> wrote: I get the following error when I tun dotplot: `ValueError Traceback (most recent call last) in () ----> 1 sc.pl.rank_genes_groups_dotplot(vitro,['MYL2'], groupby='louvain') /projects/sysbio/projects/czi/immune/anaconda2/envs/py36/lib/python3.6/site-packages/scanpy/plotting/_tools/init.py in rank_genes_groups_dotplot(adata, groups, n_genes, groupby, key, show, save, **kwds) 409 410 _rank_genes_groups_plot(adata, plot_type='dotplot', groups=groups, n_genes=n_genes, --> 411 groupby=groupby, key=key, show=show, save=save, **kwds) 412 413 /projects/sysbio/projects/czi/immune/anaconda2/envs/py36/lib/python3.6/site-packages/scanpy/plotting/_tools/init.py in _rank_genes_groups_plot(adata, plot_type, groups, n_genes, groupby, key, show, save, **kwds) 291 292 # sum(list, []) is used to flatten the gene list --> 293 gene_names = sum([list(adata.uns[key]['names'][x][:n_genes]) for x in group_names], []) 294 295 if plot_type == 'dotplot': /projects/sysbio/projects/czi/immune/anaconda2/envs/py36/lib/python3.6/site-packages/scanpy/plotting/_tools/init.py in (.0) 291 292 # sum(list, []) is used to flatten the gene list --> 293 gene_names = sum([list(adata.uns[key]['names'][x][:n_genes]) for x in group_names], []) 294 295 if plot_type == 'dotplot': ValueError: no field of name MYL2 ` Do we need to store marker genes within the adata object? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[flying-sheep]

did that help?