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Bug: the return data( prob ) from the function netVisual_bubble is not same with "cellchat@net[["prob"]]" #289

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lidd77 opened this issue Jan 10, 2025 · 0 comments

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@lidd77
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lidd77 commented Jan 10, 2025

Dear author,

  my codes is as the below : 
   dat <-  netVisual_bubble(cellchat, 
                 title.name=  paste(pathways.show.all[1], "signaling pathway L-R pairs "), 
                 signaling = pathways.show.all[1], 
                remove.isolate = TRUE, 
                return.data=TRUE)
 
  dat_prob <-  dat[["communication"]][["prob"]] 
  dat_pval <-  dat[["communication"]][["pval"]]
  
  I got the data 'dat' that is used by   netVisual_bubble to draw a picture .
  In my  understanding , for dat_prob and  dat_pval :   
             dat_prob is all  L-R  probability  between  sources and target  .
             dat_pval is    all L-R  pvalue   .between  sources and target . 

   I am not sure whether my understanding is right  ? 

   If I  was right ,    for COL6A1_ITGA3_ITGB1 between group 5 and 10 ,  so   its value in "dat_prob"   is  the same with   _cellchat@net[["prob"]]["10","5","COL6A1_ITGA3_ITGB1"]_     ?    so what happened ?  
  but I  find  it is not same ...  this value is same with  dat[["communication"]][["prob.original"]]  . 

   And     its value in  dat_pval also has same situation,    dat_pval  is not same with   cellchat@net[["pval"]]["10","5","COL6A1_ITGA3_ITGB1"]   ?   so what happened ?    I not find  pval.original ...
  
   
 Expecting your reply !

Best

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