Plot Module Trends over Pseudotime — plot_module_trends_over

Fits smoothed module-expression trajectories over pseudotime and plots module trends. If the number of points is large (> 7000 cells), the function uses a GAM-based smoothing approach for efficiency, otherwise it uses LOESS smoothing.

Usage

plot_module_trends_over_pseudotime(
  expression_list,
  pseudotime,
  module_colours = NULL,
  linewidth = 1.5,
  axis_text_size = 10,
  legend_text_size = 10,
  label_size = 10,
  show_labels = TRUE,
  smooth_threshold_max = 0.2
)

Arguments

expression_list: A list, matrix, or data frame with module expression per cell.
pseudotime: Numeric pseudotime vector.
module_colours: Optional named vector of module colours.
linewidth: Line width for smoothed trajectories.
axis_text_size: Text size for axis labels and ticks.
legend_text_size: Text size for legend labels and title.
label_size: Text size for module labels.
show_labels: Logical indicating whether module labels are shown. The labels will be located at the maximum point of the smoothed trajectory.
smooth_threshold_max: Threshold used to discard modules where the maximum value of the smoothed trajectory is below this value.

Value

A ggplot object.