Lineage Plot

Generate a lineage plot based on the pseudotime.

Usage

LineagePlot(
  srt,
  lineages,
  reduction = NULL,
  dims = c(1, 2),
  cells = NULL,
  trim = c(0.01, 0.99),
  span = 0.75,
  palette = "Dark2",
  palcolor = NULL,
  lineages_arrow = grid::arrow(length = grid::unit(0.1, "inches")),
  linewidth = 1,
  line_bg = "white",
  line_bg_stroke = 0.5,
  whiskers = FALSE,
  whiskers_linewidth = 0.5,
  whiskers_alpha = 0.5,
  aspect.ratio = 1,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  theme_use = "theme_scop",
  theme_args = list(),
  return_layer = FALSE,
  seed = 11
)

Arguments

srt: A Seurat object.
lineages: A character vector that specifies the lineages to be included. Typically, use the pseudotime of cells.
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.
trim: A numeric vector of length 2 specifying the quantile range of lineages to include in the plot.
span: The span of the loess smoother.
palette: Color palette name. Available palettes can be found in thisplot::show_palettes. Default is "Dark2".
palcolor: Custom colors used to create a color palette. Default is NULL.
lineages_arrow: An arrow object specifying the arrow for lineages.
linewidth: The linewidth for the lineages.
line_bg: A character string specifying the color for the background lines.
line_bg_stroke: The stroke width for the background lines.
whiskers: Whether to include whiskers in the plot.
whiskers_linewidth: The linewidth for the whiskers.
whiskers_alpha: The transparency for the whiskers.
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: Whether to return the plot layers as a list. Defaults is FALSE.
seed: Random seed for reproducibility. Default is 11.

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
#> ℹ [2026-01-27 07:51:40] Start standard scop workflow...
#> ℹ [2026-01-27 07:51:41] Checking a list of <Seurat>...
#> ! [2026-01-27 07:51:41] Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-01-27 07:51:41] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on the data 1/1 of the `srt_list`...
#> ℹ [2026-01-27 07:51:43] Perform `Seurat::FindVariableFeatures()` on the data 1/1 of the `srt_list`...
#> ℹ [2026-01-27 07:51:43] Use the separate HVF from srt_list
#> ℹ [2026-01-27 07:51:43] Number of available HVF: 2000
#> ℹ [2026-01-27 07:51:43] Finished check
#> ℹ [2026-01-27 07:51:44] Perform `Seurat::ScaleData()`
#> ℹ [2026-01-27 07:51:44] Perform pca linear dimension reduction
#> ℹ [2026-01-27 07:51:45] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-01-27 07:51:45] Reorder clusters...
#> ℹ [2026-01-27 07:51:45] Perform umap nonlinear dimension reduction
#> ℹ [2026-01-27 07:51:45] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ℹ [2026-01-27 07:51:49] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ✔ [2026-01-27 07:51:52] Run scop standard workflow completed
pancreas_sub <- RunSlingshot(
  pancreas_sub,
  group.by = "SubCellType",
  reduction = "UMAP",
  show_plot = FALSE
)
LineagePlot(
  pancreas_sub,
  lineages = paste0("Lineage", 1:2)
)

LineagePlot(
  pancreas_sub,
  lineages = paste0("Lineage", 1:2),
  whiskers = TRUE
)

Usage

Arguments

See also

Examples