Plots module eigengene dynamics over a pseudotime trajectory.
Usage
PlotModuleTrajectory(
seurat_obj,
pseudotime_col = "pseudotime",
n_bins = 20,
harmonized = TRUE,
ncol = 4,
point_size = 1,
line_size = 1,
se = TRUE,
group_colors = NULL,
wgcna_name = NULL
)Arguments
- seurat_obj
A Seurat object
- pseudotime_col
name of the column in seurat_obj@meta.data containing pseudotime information. Multiple names can be passed to plot multiple trajectories simultaneously.
- n_bins
number of pseudotime bins/windows used to smooth the MEs
- harmonized
logical determining whether or not to use the harmonized MEs
- point_size
size of the points in the plot
- line_size
width of the lines in the plot
- se
logical determining whether or not to show the standard error on the plot
- group_colors
optional list of colors to differentiate multiple pseudotime trajectories. Must be the same length as pseudotime_col
- wgcna_name
The name of the hdWGCNA experiment in the seurat_obj@misc slot
- n_col
number of columns for different modules in the plot