View source: R/GEX_pseudotime_trajectory_plot.R
GEX_pseudotime_trajectory_plot | R Documentation |
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)
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. |
Returns a list.Element [[1]] cell data set object with the pseudotime trajectories. Element [[2]] pseudotime trajectory plot
## Not run: ##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") ## End(Not run)
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