LineagePlot | R Documentation |
Generate a lineage plot based on the pseudotime.
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
)
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. |
RunSlingshot
CellDimPlot
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)
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