Running in pure python env: in a .py file

[DUAN-GAO]

Hello Malte,I m running in a .py file, when I tried to use scran function computeSumFactors,
that I need to convert anndata to SingleCellExperiment object,I tried following but not worked:
a = robjects.r'list'
b = robjects.r'SingleCellExperiment'
size_factors = computeSumFactors(b, clusters=input_groups)

could you help, many thanks.

[LuckyMD]

Hi @Iweirdo,

You can take the command for how to run the calculateSumFactors function (as it's now called) from #77. This function is from scran, which is an R package. So you'd need to run it in r. Try something like:

import rpy2.robjects as ro

ro.r('data') = data
adata.obs['size_factors'] = ro.r('calculateSumFactors(...)')

I haven't tested the above. This is just to give you an idea of what needs to be run in R and what in python.