LineagePlot: LineagePlot
In zh542370159/SCP: Single Cell Pipeline

LineagePlot

R Documentation

LineagePlot

Description

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 = arrow(length = 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_scp",
  theme_args = list(),
  return_layer = FALSE,
  seed = 11
)

Arguments

`srt`	An object of class Seurat.
`lineages`	A character vector that specifies the lineages to be included. Typically, use the pseudotime of cells.
`reduction`	An optional string specifying the dimensionality reduction method to use.
`dims`	A numeric vector of length 2 specifying the dimensions to plot.
`cells`	An optional character vector specifying the cells to include in the plot.
`trim`	A numeric vector of length 2 specifying the quantile range of lineages to include in the plot.
`span`	A numeric value specifying the span of the loess smoother.
`palette`	A character string specifying the color palette to use for the lineages.
`palcolor`	An optional string specifying the color for the palette.
`lineages_arrow`	An arrow object specifying the arrow for lineages.
`linewidth`	A numeric value specifying the linewidth for the lineages.
`line_bg`	A character string specifying the color for the background lines.
`line_bg_stroke`	A numeric value specifying the stroke width for the background lines.
`whiskers`	A logical value indicating whether to include whiskers in the plot.
`whiskers_linewidth`	A numeric value specifying the linewidth for the whiskers.
`whiskers_alpha`	A numeric value specifying the transparency for the whiskers.
`aspect.ratio`	A numeric value specifying the aspect ratio of the plot.
`title`	An optional character string specifying the plot title.
`subtitle`	An optional character string specifying the plot subtitle.
`xlab`	An optional character string specifying the x-axis label.
`ylab`	An optional character string specifying the y-axis label.
`legend.position`	A character string specifying the position of the legend.
`legend.direction`	A character string specifying the direction of the legend.
`theme_use`	A character string specifying the theme to use for the plot.
`theme_args`	A list of additional arguments to pass to the theme function.
`return_layer`	A logical value indicating whether to return the plot as a layer.
`seed`	An optional integer specifying the random seed for reproducibility.

Examples

data("pancreas_sub")
pancreas_sub <- RunSlingshot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", show_plot = FALSE)
LineagePlot(pancreas_sub, lineages = paste0("Lineage", 1:3))
LineagePlot(pancreas_sub, lineages = paste0("Lineage", 1:3), whiskers = TRUE)

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.