BlishLab / scriabin

Analysis of cell-cell communication at single-cell resolution
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Issue running interaction programs vignette #6

Closed emlangan closed 1 year ago

emlangan commented 1 year ago

Hi, thank you for creating this tool! I am running into an error trying to run the "Discovery of co-varying interaction programs" vignette with the panc8 dataset. It runs okay up until the InteractionPrograms() step, and then it produces the following error:

`> #find interaction programs
> panc_ip <- InteractionPrograms(panc_id, iterate.threshold = 300, cell_types = "celltype", assay = "alra")
Using database OmniPath

Iteratively generating interaction matrix
Will perform 5 iterations to approximate TOM
Error in `dplyr::sample_n()`:
! Problem while computing indices.
ℹ The error occurred in group 1: var = "acinar".
Caused by error in `sample.int()`:
! invalid 'size' argument
Run `rlang::last_error()` to see where the error occurred.
Warning message:
In size <= n || replace :
  'length(x) = 1152 > 1' in coercion to 'logical(1)'

> rlang::last_error()
<error/rlang_error>
Error in `dplyr::sample_n()`:
! Problem while computing indices.
ℹ The error occurred in group 1: var = "acinar".
Caused by error in `sample.int()`:
! invalid 'size' argument
---
Backtrace:
  1. scriabin::InteractionPrograms(...)
 18. base::local(...)
 19. base::eval.parent(substitute(eval(quote(expr), envir)))
 20. base::eval(expr, p)
 21. base::eval(expr, p)
 22. base::eval(...)
 23. base::eval(...)
 24. base::sample.int(n(), size, replace = replace, prob = NULL)
Run `rlang::last_trace()` to see the full context.`

Please let me know if you have any ideas about how to resolve this!

Thanks so much,

Erica

ajwilk commented 1 year ago

Hi Erica, Thanks much for your patience, this issue should be fixed in 7b427ad6de88c7f2e4e447dc16c4a88b044079e2 Please let me know if you run into any other issues! Best, Aaron