Update process_multiSample.py

hansenlab · Oct 9, 2024 · 96fd6c8 · 96fd6c8
1 parent d6a44b7
commit 96fd6c8
Showing 1 changed file with 2 additions and 3 deletions.
diff --git a/mNSF/process_multiSample.py b/mNSF/process_multiSample.py
@@ -165,7 +165,7 @@ def get_listSampleID(list_D_):
 
 
 
-def ini_multiSample(list_D_,L_, lik = 'nb', disp = "default"):
+def ini_multiSample(list_D_,L_, lik = 'nb', disp = "default",chol=True):
  """
  Initialize mNSF (multi-sample Non-negative Spatial Factorization).
  
@@ -198,7 +198,7 @@ def ini_multiSample(list_D_,L_, lik = 'nb', disp = "default"):
  J_=list_D_[0]["Y"].shape[1]
  for ksample in range(0,nsample_):
  D=list_D_[ksample]
- fit=pf.ProcessFactorization(J_,L_,D['Z'],psd_kernel=ker,nonneg=True,lik=lik,disp = disp)
+ fit=pf.ProcessFactorization(J_,L_,D['Z'],psd_kernel=ker,nonneg=True,lik=lik,disp = disp, chol = chol)
  fit.init_loadings(D["Y"],X=D['X'],sz=D["sz"],shrinkage=0.3)
  list_fit_.append(fit)
  if ksample==0:
@@ -345,4 +345,3 @@ def rescale_as_lda(factors,loadings,sort=False):
 
 
 
-