make_sampleqc_report: infinite or missing values in 'x'

[fansalon]

Hi there,

I am using SampleQC on my snRNAseq data. It runs overall fine, but I am experiencing some issues when trying to render the plot after having run fit_sampleqc with specific values of K_all.

Below is the code I am using:

qc_dt <- make_qc_dt([email protected], 
                     sample_var  = 'orig.ident', 
                     qc_names    = c('log_counts', 'log_feats', 'logit_mito'),
                     annot_vars  = 'orig.ident')
                     
qc_obj <- calc_pairwise_mmds(qc_dt, 
                              qc_names = c('log_counts', 'log_feats', 'logit_mito'), 
                              annots_disc = 'orig.ident',
                              annots_cont = NULL)

The above runs with no issue.

Similarly, if I run:

qc_obj <- fit_sampleqc(qc_obj, K_all=1)
proj_name ='whatever'
save_dir  = qcdir
make_sampleqc_report(qc_obj, save_dir, proj_name)

Everything runs fine.

The error arises when I set K_all=3 and I re-run the bunch of code above.
What I get is the following error:

Quitting from lines 90-96 [plot_alpha_j_likes] (SampleQC_report_template.Rmd)
Something went wrong with rendering your report :/
Here's the original error message:
infinite or missing values in 'x'
[1] NA

Do you know where the problem is / how I could solve this?

Thanks,
Federico