About silhouetteRankTest

[nnnanchen]

Hi, I have been running Giotto on DLPFC dataset SpatialLIBD

# create spatial network
visium_brain <- createSpatialNetwork(gobject=visium_brain, 
                                     method='kNN', 
                                     k=5, 
                                     maximum_distance_knn=400, 
                                     name='spatial_network')

## silhouette
spatial_genes=silhouetteRankTest(visium_brain, 
                                 overwrite_input_bin=F, 
                                 output=file.path(dir.output, "sil.result"), 
                                 matrix_type="dissim", 
                                 num_core=20, 
                                 parallel_path = "/usr/local/bin/",
                                 verbose=T, 
                                 expression_values="normalized", 
                                 query_sizes=10)

### cluster the top 1500 spatial genes into 20 clusters
ext_spatial_genes=spatial_genes[1:1500,]$gene

Error Message

silhouette

spatial_genes=silhouetteRankTest(visium_brain,

• overwrite_input_bin=F,
• .... [TRUNCATED] Error in py_call_impl(callable, call_args$unnamed, call_args$named) : OSError: [WinError 6] 句柄无效。 Run reticulate::py_last_error() for details.

  
  ── Python Exception Message ───────────────────────────────────────────────────────────────────────────────────────────────────────
  Traceback (most recent call last):
  File "D:/Software/R/R-4.3.3/R-4.3.3/library/Giotto/python/silhouette_rank_wrapper.py", line 46, in silhouette_rank
  prep.do_one(args1)
  File "C:\Users\nanchen\AppData\Local\R-MINI~1\envs\GIOTTO~1\lib\site-packages\silhouetteRank\prep.py", line 155, in do_one
  result = subprocess.call("Rscript --version 2> /dev/null", shell=True)
  File "C:\Users\nanchen\AppData\Local\R-MINI~1\envs\GIOTTO~1\lib\subprocess.py", line 345, in call
  with Popen(*popenargs, **kwargs) as p:
  File "D:\Software\R\R-4.3.3\R-4.3.3\library\reticulate\python\rpytools\subprocess.py", line 15, in __init__
  return og_Popen__init__(self, *args, **kwargs)
  File "C:\Users\nanchen\AppData\Local\R-MINI~1\envs\GIOTTO~1\lib\subprocess.py", line 832, in __init__
  errread, errwrite) = self._get_handles(stdin, stdout, stderr)
  File "C:\Users\nanchen\AppData\Local\R-MINI~1\envs\GIOTTO~1\lib\subprocess.py", line 1285, in _get_handles
  c2pwrite = _winapi.GetStdHandle(_winapi.STD_OUTPUT_HANDLE)
  OSError: [WinError 6] 句柄无效。

── R Traceback ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────── ▆

1. ├─base::source("C:/Users/nanchen/Downloads/DLPFC_Giotto.R", echo = TRUE)
2. │ ├─base::withVisible(eval(ei, envir))
3. │ └─base::eval(ei, envir)
4. │ └─base::eval(ei, envir)
5. └─Giotto::silhouetteRankTest(...) at nanchen/Downloads/DLPFC_Giotto.R:84:1
6. └─reticulate (local) silhouette_rank(...)
7. └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named) Screenshots

System Information

• OS: windows
• Version
  • R-4.3.3
  • Giotto-4.0.4
  • Python-3.10.2
  • silhouetteRank 1.0.5.13
  • eva 0.2.6