ValueError: too many values to unpack (expected 2)

[OMIC-coding]

I encountered a bug called ValueError: too many values to unpack (expected 2) when I runned the following codes:

Construct the flow expression matrices

commot_output_key = 'commot-CellPhoneDB_v4.0'
fs.pp.construct_flows_from_commot(adata,
commot_output_key=commot_output_key,
gem_expr_key='X_gem',
scale_gem_expr=True,
flowsig_network_key='flowsig_network',
flowsig_expr_key='X_flow'
)
The information of the used adata is as follows:
AnnData object with n_obs × n_vars = 4893 × 1844
obs: 'in_tissue', 'array_row', 'array_col', 'n_genes', 'n_counts', 'MITF_regulon'
var: 'gene_ids', 'feature_types', 'genome', 'highly_variable', 'means', 'dispersions', 'dispersions_norm'
uns: 'spatial', 'log1p', 'hvg', 'commot-CellPhoneDB_v4.0-info', 'nsf_info'
obsm: 'spatial', 'commot-CellPhoneDB_v4.0-sum-sender', 'commot-CellPhoneDB_v4.0-sum-receiver', 'X_gem'
layers: 'count'
obsp: 'commot-CellPhoneDB_v4.0-SPP1-CD44', 'commot-CellPhoneDB_v4.0-LGALS9-CD44', 'commot-CellPhoneDB_v4.0-LGALS9-SLC1A5', 'commot-CellPhoneDB_v4.0-CCL4L2-VSIR', 'commot-CellPhoneDB_v4.0-FGF2-CD44', 'commot-CellPhoneDB_v4.0-nan', 'commot-CellPhoneDB_v4.0-total-total'

[axelalmet]

Hi Joey,

Thanks for your interest in FlowSig! I checked the code and found some errors in the functions used to construct the inflow variables. I'm so sorry about that!

I have fixed these changes and updated the repository. Please could you update the installation to the latest version and let me know if that works? Thank you!

Best wishes,
Axel.

[OMIC-coding]

Thanks for your prompt reply, this step works now. However, I'm wondering if it's possible for you to provide some guidance on visualization of the flow_network, especially for the spatial transcriptomic part~

[axelalmet]

Hi Joey,

Sorry for the late reply. My plan is to update the repository to include the functions to generate the visualisations done in the paper and notebooks with visualisation examples. But effectively, if you have experience with NetworkX, we use the adjacency matrices to construct a DirectedGraph, e.g., via this function, which we then visualise as multipartite networks.

I'll try to update the repository by the end of week/start of next week!