How to add metadata to stereopy object

[GokceOGUZ]

I have few questions related to cluster annotation

1. I performed basic processing in stereopy and clustered the data. We want to annotate the clusters and in the process merge any clusters that are similar. However, I am getting the error message "Categorical categories must be unique" (see screenshot and brief code below):

annotation_dict = {
    '1':'a',
    '2':'b',
    '3':'c',
    '4':'c',
    '5':'c',
    }

data.tl.annotation(
        annotation_information=annotation_dict, 
        cluster_res_key='louvain', 
        res_key='anno_louvain'
  )

2. I exported the data to R and performed subclustering there. I created a mapping file that contains the bin id and my desired grouping. How can I read and add this to the metadata of the stereopy object?

3. I want to annotate some bins as a cell type manually if their expression levels for a gene is high. i.e. not using/overriding the cluster information.

Any advice is much appreciated.

[tanliwei-coder]

Hi!

1. data.tl.annotation only can support one to one.
2. you can save the data as an anndata format file(h5ad) and save the groups into obs, then read it by data = st.io.read_h5ad('xxx.h5ad'), after reading, you can get the groups from data.cells[obs_key], the obs_key is the key of groups stored in anndata.obs.
3. about annotation, you can refer to here.