Trajectory Plot (Pseudotime)

Creates pseudotime trajectory plots on dimension reduction coordinates. Overlays a principal curve representing the differentiation trajectory with pseudotime color mapping on top of cell scatter points.

Usage

TrajectoryPlot(
  data,
  dims = 1:2,
  pseudotime = NULL,
  group_by = NULL,
  group_by_sep = "_",
  branches = NULL,
  curve_data = NULL,
  curve_size = 1.2,
  curve_arrow = TRUE,
  pt_size = NULL,
  pt_alpha = 0.6,
  bg_color = "grey80",
  pseudotime_palette = "Spectral",
  split_by = NULL,
  split_by_sep = "_",
  facet_by = NULL,
  facet_scales = "fixed",
  facet_nrow = NULL,
  facet_ncol = NULL,
  facet_byrow = TRUE,
  theme = "theme_ggforge_grid",
  theme_args = list(),
  palette = "forge",
  palcolor = NULL,
  alpha = 1,
  aspect.ratio = 1,
  legend.position = "right",
  legend.direction = "vertical",
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  seed = 8525,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  axes = NULL,
  axis_titles = NULL,
  guides = NULL,
  design = NULL,
  ...
)

Arguments

data: A data frame containing the data to plot
dims: Column names or indices for dimensions (x, y).
pseudotime: Column for pseudotime values (continuous).
group_by: Column for cell type grouping (shown as point color when pseudotime is mapped to a separate curve overlay).
group_by_sep: Separator for multiple group_by columns.
branches: Column indicating branch assignment (optional).
curve_data: Optional data frame with curve coordinates (x, y columns matching dims). If NULL, a LOESS smooth through data is used.
curve_size: Line width for trajectory curve.
curve_arrow: Whether to add arrow to curve.
pt_size: Point size.
pt_alpha: Point transparency.
bg_color: Background point color.
pseudotime_palette: Palette for pseudotime gradient.
split_by: Column name(s) to split data into multiple plots
split_by_sep: Separator when concatenating multiple split_by columns
facet_by: Column name(s) for faceting the plot
facet_scales: Scales for facets: "fixed", "free", "free_x", "free_y"
facet_nrow: Number of rows in facet layout
facet_ncol: Number of columns in facet layout
facet_byrow: Fill facets by row (TRUE) or column (FALSE)
theme: Theme name (string) or theme function
theme_args: List of arguments passed to theme function
palette: Color palette name
palcolor: Custom colors for palette
alpha: Transparency level (0-1)
aspect.ratio: Aspect ratio of plot panel
legend.position: Legend position: "none", "left", "right", "bottom", "top"
legend.direction: Legend direction: "horizontal" or "vertical"
title: Plot title
subtitle: Plot subtitle
xlab: X-axis label
ylab: Y-axis label
seed: Random seed for reproducibility
combine: Whether to combine split plots into one
nrow: Number of rows when combining plots
ncol: Number of columns when combining plots
byrow: Fill combined plots by row
axes: How to handle axes in combined plots ("keep", "collect", "collect_x", "collect_y")
axis_titles: How to handle axis titles in combined plots
guides: How to handle guides in combined plots ("collect", "keep", "auto")
design: Custom layout design for combined plots
...: Additional arguments passed to atomic plotting functions.

Value

A ggplot object or combined plots

Examples

# \donttest{
set.seed(42)
n <- 300
t <- seq(0, 2 * pi, length.out = n)
data <- data.frame(
  UMAP1 = t + rnorm(n, 0, 0.3),
  UMAP2 = sin(t) + rnorm(n, 0, 0.3),
  pseudotime = seq(0, 1, length.out = n),
  cluster = sample(c("A", "B", "C"), n, replace = TRUE)
)
TrajectoryPlot(data, dims = 1:2, pseudotime = "pseudotime")

# }

Usage

Arguments

Value

See also

Examples