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Plot Palantir trajectories

Source: R/PalantirTrajectoryPlot.R
PalantirTrajectoryPlot.Rd

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

Which dimensionality reduction to use. If not specified, will use the reduction returned by DefaultReduction.

dims

Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions

cells

A character vector of cell names to use.

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

Color palette name. Available palettes can be found in thisplot::show_palettes. Default is "Chinese".

palcolor

Custom colors used to create a color palette. Default is NULL.

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

Aspect ratio of the panel. Default is 1.

title

The text for the title. Default is NULL.

subtitle

The text for the subtitle for the plot which will be displayed below the title. Default is NULL.

xlab

The x-axis label of the plot. Default is NULL.

ylab

The y-axis label of the plot. Default is NULL.

legend.position

The position of legends, one of "none", "left", "right", "bottom", "top". Default is "right".

legend.direction

The direction of the legend in the plot. Can be one of "vertical" or "horizontal".

theme_use

Theme used. Can be a character string or a theme function. Default is "theme_scop".

theme_args

Other arguments passed to the theme_use. Default is list().

return_layer

Logical. If TRUE, returns ggplot2 layers instead of a complete plot.

seed

Random seed for reproducibility. Default is 11.

verbose

Whether to print the message. Default is TRUE.

See also

RunPalantir, FeatureDimPlot, CellDimPlot

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- standard_scop(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)
)
} # }