draw_trajectory_plot {SCORPIUS}

Visualise SCORPIUS

Description

draw_trajectory_plot is used to plot samples after performing dimensionality reduction. Additional arguments can be provided to colour the samples, plot the trajectory inferred by SCORPIUS, and draw a contour around the samples.

Usage

draw_trajectory_plot(
  space,
  progression_group = NULL,
  path = NULL,
  contour = FALSE,
  progression_group_palette = NULL,
  point_size = 2,
  point_alpha = 1,
  path_size = 0.5,
  path_alpha = 1,
  contour_alpha = 0.2
)

Arguments

space

A numeric matrix or a data frame containing the coordinates of samples.

progression_group

NULL or a vector (or factor) containing the groupings of the samples (default NULL).

path

A numeric matrix or a data frame containing the coordinates of the inferred path.

contour

TRUE if contours are to be drawn around the samples.

progression_group_palette

A named vector palette for the progression group.

point_size

The size of the points.

point_alpha

The alpha of the points.

path_size

The size of the path (if any).

path_alpha

The alpha of the path (if any).

contour_alpha

The alpha of the contour (if any).

Value

A ggplot2 plot.

Examples

## Generate a synthetic dataset
dataset <- generate_dataset(num_genes = 500, num_samples = 300, num_groups = 4)
space <- reduce_dimensionality(dataset$expression, ndim = 2)
groups <- dataset$sample_info$group_name

## Simply plot the samples
draw_trajectory_plot(space)

## Colour each sample according to its group
draw_trajectory_plot(space, progression_group = groups)

## Add contours to the plot
draw_trajectory_plot(space, progression_group = groups, contour = TRUE)

## Plot contours without colours
draw_trajectory_plot(space, contour = TRUE)

## Infer a trajectory and plot it
traj <- infer_trajectory(space)
draw_trajectory_plot(space, progression_group = groups, path = traj$path)
draw_trajectory_plot(space, progression_group = groups, path = traj$path, contour = TRUE)

## Visualise gene expression
draw_trajectory_plot(space, progression_group = dataset$expression[,1])