How to force Monocle to use a specifc cluster as the starting/ending point

[kaizen89]

Hello, I am using Monocle2 and I want to order my cells allong a trajectory of activation, the problem is that I know biologically that one specific cluster shoud be at the end of the trajectory but Monocle is putting this cluster just before the last one. The trajectory is mainly driven by a set of genes that are upregulated during pseudotime but biologically the genes shoud be downregulated at later time points & Monocle does not seem to handle well this kind of scenario. Is there a way to force Monocle to put this cluster as the ending point?

[McStber]

Hi kaizen89,

Indeed thats a good question! The only thing I know is the parameter "root_cell" for ordering the cells were you can name a cell to use as the root of the ordering tree:

orderCells(cds, num_paths = 1, reverse = FALSE, root_cell = NULL)

But to set a cell group as an endpoint I don't know, maybe Monocle developers can help?

Best, Michael

[honghh2018]

Hi @McStber, The orderCells function had no the parameter root_cell，i wonder where you find this parameter in monocle2 ? Could you point out where this parameter can be found in monocle2 orderCells? Best, hanhuihong

[JialiYue]

Hi @McStber, The orderCells function had no the parameter root_cell，i wonder where you find this parameter in monocle2 ? Could you point out where this parameter can be found in monocle2 orderCells? Best, hanhuihong In monocle3