Hi @ClarkGregg sorry for the delay in response. I will answer your questions in the following:
I am wondering, **(1)** if the 'pre-branch' state is comprised of all states excepted for the two being tested or just state 2, in this particular case. And also **(2)** what is the 'pre-branch' if I try to compare states that sit within different branches, say, branch 4 and branch 7.
(1): In fact, BEAM tries to traverse backward from the cell on the branch point all the way back to the root cell (the cell with pseudotime 0) and use all those cells as the the pre-branch. So either of what you are thinking is not exactly right. So the pre-branch includes cells from state 2, 3, 5 if I read the color correctly
(2): This is a very good question since state 4 relates to branch point 2 while state 7 relates to branch point 3. For this test, the pre-branch will only include cells from state 2.
My question 2 is about a parameter, the parameter inside plot_genes_branched_heatmap() called branch_label. the default branch label is 'cell fate 1' and 'cell fate 2'. How do I map these labels to the corresponding branches being tested? For example, if I am comparing branch 1 and branch 7. should 'cell fate 1' correspond to branch 1 and branch 7 correspond to 'cell fate 2' ?
I think that is right. Cell fate 1 corresponds to the state with small id (in this case, state 1) while cell fate 2 corresponds to sate with bigger id (in this case, state 2)

Hello,
Thank you for your clarifications,

Following your explanation of BEAM

(1): In fact, BEAM tries to traverse backward from the cell on the branch point all the way back to the root cell (the cell with pseudotime 0) and use all those cells as the the pre-branch.

So pre-branch in case of testing node 3 should rather be the state 1 branch as it is leading towards pseudotime 0 ?

Hello,
when I'm doing pseudotime analysis with monocle, there also is something strange I don't understand. First, I want to know what's the meaning of Y-18 and Y-8 in the plot_genes_branched_pseudotime graph. Secondly, I didn't get symmetric group in plot_genes_branched_heatmap when I used "BEAM_res_branch1<-BEAM(HSMM_myo, branch_point = 4, cores = 1) ". Please tell why!


Here is the state.

Hi@Xiaojieqiu. Sincere thanks for your explanation. May I ask why the pre-branch will only include cells from state 2 when testing for the difference between state4 and state7. Thanks!

(2): This is a very good question since state 4 relates to branch point 2 while state 7 relates to branch point 3. For this test, the pre-branch will only include cells from state 2.

I have same question. Why only state 2 is the pre-branch?