Hi Zhicheng Ji,

     When I use the TSCAN on my data, I find there are two problems. 

(1) The plotmclust() function cannot draw all edges in the figure. For example, there are 14 clusters after using the exprmclust() function. When using  plotmclust(mclustobj = lpsmclust, show_cell_names=FALSE), there are 4 isolated clusters which not have connections with other clusters number.  Is there any parameter wrong in my functions? 

 (2) Next, I intend to use the TSCANorder() function to get the cells orders, 

lpsorder <- TSCANorder(mclustobj = lpsmclust, MSTorder = NULL, orderonly = T, flip = F, listbranch = F)

But the number of elements in lpsorder is 10404 , however, the number of elements in lpsmculst is 21005. 

I am very puzzled by the results. Can you help me to explain it? 

Many thanks.

Best regards,

Yang Chen