immucellai2 2.1.31__py3-none-any.whl → 2.1.33__py3-none-any.whl

immucellai2/Deconvolution.py

@@ -256,17 +256,18 @@ def MainRun(RunObject, seed=42, MultithreadModule = 'joblib'):
     EnvironmentRun = RunObject.EnvironmentRun 
     RecordTime = CLASS_FOR_TIME() 
     nsamples = len(RunObject.SampleList) 
+    SampleNameToIndex = {name: idx for idx, name in enumerate(RunObject.SampleList)}
     parameterlist = []
-    #CelltypesReferenceMatrix = RunObject.CelltypesReferenceMatrix 
-    for sample_index in range(nsamples):
-        SampleName = RunObject.SampleList[sample_index]
+    for SampleNameii in range(nsamples):
+        SampleName = RunObject.SampleList[SampleNameii]
+        SampleIndex = SampleNameToIndex[SampleName]  
         parameterlist.append((
-            (RunObject.EmceeParameter).mycopy(),
-            RunObject.CelltypesReferenceMatrix ,
-            RunObject.SamplesBulkRNAseqExpression[sample_index],
-            RunObject.SampleList[sample_index], 
-            RunObject.MAPorMLE 
-        )) 
+            RunObject.EmceeParameter.mycopy(),
+            RunObject.CelltypesReferenceMatrix,
+            RunObject.SamplesBulkRNAseqExpression[SampleIndex],  
+            SampleName,
+            RunObject.MAPorMLE
+        ))
     MultiprocessingReturnValue = []
     if MultithreadModule == 'joblib':
        try:

immucellai2/myclasses.py

@@ -99,16 +99,10 @@ class CLASS_FOR_RUNRESULT(object):
             self.EmceeFunction2( McSamplingResultList[sampleii, :, :, :] )
       return  NewMcSamplingResultList
    def optimized_calculation(self, FlatSamplingResultOne, nCellType):
-      row_sums = FlatSamplingResultOne.sum(axis=1, keepdims=True)
-      row_sums_safe = row_sums + 1e-10 
-      if FlatSamplingResultOne.shape[1] == nCellType:
-         return FlatSamplingResultOne / row_sums_safe
-      elif FlatSamplingResultOne.shape[1] + 1 == nCellType:
-         normalized = FlatSamplingResultOne / row_sums_safe
-         last_col = 1 - normalized.sum(axis=1, keepdims=True)
-         return numpy.column_stack((normalized, last_col))
-      else:
-         raise ValueError(f"Dimension mismatch: input {FlatSamplingResultOne.shape[1]} columns, target {nCellType}columns")
+       if FlatSamplingResultOne.shape[1] == nCellType:
+           return FlatSamplingResultOne / FlatSamplingResultOne.sum(axis=1)[:, None]
+       elif FlatSamplingResultOne.shape[1] + 1 == nCellType:
+           return numpy.column_stack((FlatSamplingResultOne, 1 - FlatSamplingResultOne.sum(axis=1)))
    def EmceeFunction2(self, FlatSamplingResultList): 
       fshape = FlatSamplingResultList.shape
       nCellType = len(self.CellType)

{immucellai2-2.1.31.dist-info → immucellai2-2.1.33.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: immucellai2
-Version: 2.1.31
+Version: 2.1.33
 Summary: A tool for immune cell type deconvolution
 Home-page: https://github.com/VyvyanYjm/ImmuCellAI2.0
 Author: YangJingmin

{immucellai2-2.1.31.dist-info → immucellai2-2.1.33.dist-info}/RECORD

@@ -1,16 +1,16 @@
-immucellai2/Deconvolution.py,sha256=Ai3cE_YhVXyu5OWymnNbRqGWUHdXiTE8FVSmu5pdNvM,12507
+immucellai2/Deconvolution.py,sha256=HoG-kT3dkMfDpJVMunihv2Qp0P4OnOpPwKj5e9EDTg8,12549
 immucellai2/Drawplot.py,sha256=YnUleceEyim9SsTiU18mbAMcjOH9ovBXJW3pwXxA7as,5136
 immucellai2/ObtainCategory.py,sha256=N1F_yUHoaIisnlms4aNNJ2UIzZDI2TIc0t7IRLtM7So,7008
 immucellai2/PrepareData.py,sha256=tJWtQbfFfXszAQMnAmyzFrXB40wgHl48WP3WZKfeifg,5935
 immucellai2/Time.py,sha256=et3aAqyVDKwP5_tdGIwA6yxdXRbbYemc9wEaPHpQCck,572
 immucellai2/__init__.py,sha256=wi7UznfkskCvT4yj-u1RuyN0SK1tZptpXffIaQW2XkQ,3055
-immucellai2/myclasses.py,sha256=9Rgil00HX_RfOhvpdvUZDsvFi7RdIfXay4V3lRcQsQ8,12409
+immucellai2/myclasses.py,sha256=LFVMgIwraRrw_uv4g5BG-799AiH3apHXc-mBlAlYRd4,12120
 immucellai2/myconfig/Celltype.category,sha256=l_5vspGpyDbuaQ7QOLIQjSs4xb6x6_pvvtnP709CVzQ,5530
 immucellai2/myconfig/MarkerUsedDeconvolution.txt,sha256=33gCFD1_Clis7NFaQTUHc5s7BXoN61jWgWPgjT-m0n0,60756
 immucellai2/myconfig/reference_normalCelltypes.txt,sha256=zhKP5Z1TgVyB6ijIamjM1ETmuwQgRATofO-0ds89gP4,39107049
 immucellai2/myconfig/reference_tumorCelltypes.txt,sha256=xYgjehHIXb5re20bmXeoqxfyvQmgpr4y-0ysCVnEeI8,40893156
-immucellai2-2.1.31.dist-info/METADATA,sha256=SCPG7R6NhSKAaAkxPkANPa8LVvs4O2owcR-GB6U4FYg,1662
-immucellai2-2.1.31.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-immucellai2-2.1.31.dist-info/entry_points.txt,sha256=asskhaErD37JB_X_4TPB1itaIytWCU-RHFIyVGQ8Jbw,62
-immucellai2-2.1.31.dist-info/top_level.txt,sha256=9r84YbXmTdnKZnK2OGrTsgYPFoSBdk4EkeieDg-7_DY,12
-immucellai2-2.1.31.dist-info/RECORD,,
+immucellai2-2.1.33.dist-info/METADATA,sha256=Hsc5rzIfRogH5piGI4G5uYmLXZ901M5JyTPpMA03yY4,1662
+immucellai2-2.1.33.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+immucellai2-2.1.33.dist-info/entry_points.txt,sha256=asskhaErD37JB_X_4TPB1itaIytWCU-RHFIyVGQ8Jbw,62
+immucellai2-2.1.33.dist-info/top_level.txt,sha256=9r84YbXmTdnKZnK2OGrTsgYPFoSBdk4EkeieDg-7_DY,12
+immucellai2-2.1.33.dist-info/RECORD,,