This function plots pseudotime along the trajectories which have been constructed with the GEX_trajectories() function.

This function plots pseudotime along the trajectories which have been constructed with the GEX_trajectories() function.

GEX_pseudotime_trajectory_plot(cds, root.nodes, monocle.version, root.state)

Arguments

cds

cell data set object. Output element [[1]] of the GEX_trajectories() function

root.nodes

For monocle3: Root nodes to determine for the pseudotime trajectories. GEX_trajectories output [[3]] yields all the possible root nodes. Choose the ones you like.

monocle.version

Version of monocle. Either monocle2 or monocle3. Has to be the same as in GEX_trajectories().Default is monocle3.

root.state

For monocle2: Root state to determine starting cluster for the pseudotime trajectories. GEX_trajectories ouput [[3]] yields all the possible root states Choose the one you like.

Value

Returns a list.Element [[1]] cell data set object with the pseudotime trajectories. Element [[2]] pseudotime trajectory plot

Examples

if (FALSE) {
##monocle3
pseudotime_output <- GEX_pseudotime_trajectory_plot(
GEX_trajectories_output[[1]], root.nodes = c('Y_742','Y_448','Y_964') )

##monocle2
pseudotime_output <- GEX_pseudotime_trajectory_plot(
GEX_trajectories_output[[1]], monocle.version = 'monocle3', root.state = "2")
 }