Plot Palantir trajectories

Plot branch-aware Palantir trajectories on a two-dimensional embedding.

Usage

PalantirTrajectoryPlot(
  srt,
  reduction = NULL,
  dims = c(1, 2),
  cells = NULL,
  pseudotime_key = "palantir_pseudotime",
  branch_cols = NULL,
  diff_potential_key = "palantir_diff_potential",
  pseudotime_interval = c(0, 1),
  branch_min_prob = 0.05,
  n_bins = 60,
  min_cells_per_bin = 3,
  smooth = TRUE,
  trajectory_method = c("loess", "bin"),
  smoothness = 1,
  span = 0.75,
  n_path_points = 200,
  cell_color = "pseudotime",
  pt.size = 0.5,
  pt.alpha = 0.8,
  palette = "Dark2",
  palcolor = NULL,
  trajectory_palette = "Dark2",
  trajectory_palcolor = NULL,
  trajectory_linewidth = 1.2,
  trajectory_bg = "black",
  trajectory_bg_stroke = 0.7,
  trajectory_arrow = grid::arrow(length = grid::unit(0.12, "inches"), type = "closed"),
  aspect.ratio = 1,
  title = "Palantir",
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  theme_use = "theme_scop",
  theme_args = list(),
  return_layer = FALSE,
  seed = 11,
  verbose = TRUE
)

Arguments

srt: A Seurat object.
reduction: Reduction to plot. NULL uses DefaultReduction.
dims: Length-2 vector of dimensions to plot.
cells: Cell names to include.
pseudotime_key: Name of the metadata column containing Palantir pseudotime.
branch_cols: Metadata columns containing Palantir branch probabilities. If NULL, columns ending with "_diff_potential" are used, excluding pseudotime_key and diff_potential_key.
diff_potential_key: Name of the Palantir entropy/differentiation potential column to exclude from branch auto-detection.
pseudotime_interval: Numeric vector of length 2 specifying the pseudotime range to plot.
branch_min_prob: Minimum branch probability used to select cells for a branch trajectory.
n_bins: Number of pseudotime bins used to summarize each trajectory.
min_cells_per_bin: Minimum number of cells required in a bin.
smooth: Whether to smooth the trajectory with stats::loess.
trajectory_method: Method used to fit trajectory coordinates along pseudotime. "loess" uses a fully R-native smoother over a Palantir-style pseudotime grid; "bin" uses binned median coordinates.
smoothness: Smoothing multiplier for the R-native loess span. Higher values yield smoother curves.
span: Base span used for loess smoothing.
n_path_points: Number of pseudotime points used to draw each smoothed trajectory.
cell_color: Cell coloring mode. Use "pseudotime" for Palantir pseudotime, "branch_selection" for the branch with highest probability, "none" to hide cell coloring, or any metadata column.
pt.size: Point size for cells.
pt.alpha: Point alpha for cells.
palette, palcolor: Palette name (thisplot::show_palettes) or custom colors.
trajectory_palette: Color palette for trajectories.
trajectory_palcolor: Custom colors for trajectories.
trajectory_linewidth: Line width of trajectories.
trajectory_bg: Color for the trajectory background stroke.
trajectory_bg_stroke: Width added to the trajectory background stroke.
trajectory_arrow: Arrow used for trajectories. See grid::arrow.
aspect.ratio: Panel aspect ratio.
title, subtitle, xlab, ylab: Plot labels.
legend.position: Legend placement ("none", "left", "right", "bottom", "top"), direction, and title. legend.title = NULL uses the group name.
legend.direction: Legend direction: "horizontal" or "vertical".
theme_use, theme_args: Theme name or function, plus extra theme arguments.
return_layer: Logical. If TRUE, returns ggplot2 layers instead of a complete plot.
seed: Random seed.
verbose: Whether to print messages.

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
pancreas_sub <- RunPalantir(
  pancreas_sub,
  group.by = "SubCellType",
  linear_reduction = "PCA",
  nonlinear_reduction = "UMAP",
  early_group = "Ductal",
  terminal_groups = c("Alpha", "Beta", "Delta", "Epsilon")
)
PalantirTrajectoryPlot(
  pancreas_sub,
  reduction = "UMAP",
  pseudotime_interval = c(0, 0.9)
)
PalantirTrajectoryPlot(
  pancreas_sub,
  reduction = "UMAP",
  cell_color = "branch_selection",
  pseudotime_interval = c(0, 0.9)
)
} # }

Usage

Arguments

See also

Examples