Documentation of "branch_states" and "branch_labels" arguments
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kevin.rue ▴ 300
@kevinrue-6757
Last seen 4 months ago
University of Oxford

Dear developers,

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.

First question:
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)?

Second question:
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!

Kind regards
Kevin

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