kkbarratt19
commented
1 year ago Hi Sayyam
I'm not sure if you ever found an answer to this. I suggest that you play around with the ncenter parameters to increase or decrease the complexity and number of branches in your trajectory.
e.g. learn_graph(You_Monocle3_object, use_partition = TRUE, verbose = FALSE, learn_graph_control=list(ncenter=X)) where X can be any number that you want (I've seen a lot of people use ncenter=1000 in their example codes).
The problem is that I can't find any documentation that explains what ncenter does. I was hoping to piggy-back off your post and find someone here that could answer for us both. Specifically, I'd like to know:
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if you do not include learn_graph_control=list(ncenter=) in your code, what is the default ncenter value that is used to calculate the trajectory?
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what is the ncenter value actually referring to? I saw a suggestion somewhere that it was the number of cells that learn_graph uses to calculate the trajectory, so a lower ncenter number = a less complex trajectory as it is uses fewer cells, however I could not find this suggestion confirmed anywhere.
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how do we know the optimal ncenter value to use for our data? In my own data a ncenter value of 650 generates a completely different major branch point compared to using 640 or 660. There is no current biological data that can tell me which is the most likely trajectory.
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If we have two different cohorts (untreated vs treated) and we are trying to compare trajectory changes between the cohorts, it is best practice to use the same ncenter value for both cohorts or should the ncenter be modified for the number of cells in each cohort?
Fingers crossed somone can answer or direct me to the answer in the Monocle3 documentation.
Hello @hpliner,
Thank you for the amazing tool. I am running monocle3 on hematopoietic cells to track trajectory from the HSC. However, I noticed monocle3 did not draw branches between certain cell types (ex. LMPP to MLP), contradicting theoretical predictions. How can I manipulate the learn_graph function to "force" these branches?