CHOIR Fails with Leiden Clustering

[marcobuttigieg]

Hello,

Thank you so much for your work on CHOIR, it's a really excellent tool that I would like to start using more frequently.

I have been able to successfully implement CHOIR using the default settings, however, when trying to use Leiden clustering with cluster_params = list(algorithm = 4, group.singletons = TRUE), the code fails while identifying the starting resolution as this relies on running clustering with resolution=0, which leidenbase cannot accomodate. See the error below:

sobj <- CHOIR(sobj,
               use_assay = 'RNA',
               cluster_params = list(
                 algorithm = 4, 
                 group.singletons = TRUE)
               )

(Step 4/7) Identify starting clustering resolution..
Error in leidenbase::leiden_find_partition(input, partition_type = partition.type,  : 
  input parameter error(s):
  -> resolution_parameter <= 0

Is there a way to avoid using a starting resolution of 0 when trying to apply Leiden clustering? Thanks for your help!!