Pandas to Anndata?

[rgranit]

Hey all,

Is there an option to convert Pandas df to Anndata object?

Thanks,
Roy

[rgranit]

I think I might have figured it out, but confirmation would help:

# dataframe for annotating the observations
obs = pd.DataFrame()
obs['sample'] = df.columns
var_names = df.index
# dataframe for annotating the variables
var = pd.DataFrame(index=var_names)
# the data matrix 
X = df.T.values
adata = anndata.AnnData(X, obs=obs, var=var, dtype='int32')

output:
AnnData object with n_obs × n_vars = 10 × 24514 obs: 'sample'

[ivirshup]

You could just pass the dataframe directly to the anndata constructor, but you'll only get X, obs_names, and var_names.

Here's an example:

import scanpy as sc, anndata as ad

pbmc = sc.datasets.pbmc68k_reduced()

pbmc.to_df().head()

index              HES4  TNFRSF4  SSU72  PARK7   RBP7    SRM  MAD2L2  AGTRAP  \
index                                                                          
AAAGCCTGGCTAAC-1 -0.326   -0.191 -0.728 -0.301  3.386 -0.531   2.016   3.377   
AAATTCGATGCACA-1  1.171   -0.191  0.795 -1.200 -0.174 -0.531   1.889  -0.486   
AACACGTGGTCTTT-1 -0.326   -0.191  0.483 -1.200 -0.174 -0.531  -0.451   0.971   
AAGTGCACGTGCTA-1 -0.326   -0.191  1.134 -0.157 -0.174 -0.531  -0.451  -0.486   
ACACGAACGGAGTG-1 -0.326   -0.191 -0.728 -0.607 -0.174 -0.531  -0.451   0.787
...

ad.AnnData(pbmc.to_df())

AnnData object with n_obs × n_vars = 700 × 765