PlotModuleTrajectory — PlotModuleTrajectory • hdWGCNA

Plots module eigengene dynamics over a pseudotime trajectory.

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