First of all thank you for the great work behind `monocle`. Much appreciated!
I am using `BEAM`, `plot_genes_branched_heatmap`, and `plot_genes_branched_pseudotime` at the moment. I am struggling to interpret which two branches are compared, and how to control it.
In the case where "branch_point = N" is given, I would intuitively assume that the two branches _downstream_ from N in terms of _pseudotime_ are compared, right? Even so, how do I know which of the two branches are assigned the names of 'Cell fate 1' and 'Cell fate 2' (apart from manually running buildBranchCellDataSet and checking out which of the two branches has higher expression)?
I cannot figure out how to specify the "branch_states" and "branch_labels" in any function. I keep getting an error message that I tracked back to the `igraph` package:
> BEAM_res <- BEAM( + HSMM, cores = 4, + branch_states = c(2, 3), branch_labels = c("Activated", "Latent") + ) Error in as.igraph.vs(graph, from) : Invalid vertex names
I genuinely cannot understand the documentation about those two options and how to find valid values for them (I use the devel version 2.5.0).
Any advice welcome, I hope I'm not missing something obvious!