plot_cells_3d: Plot a dataset and trajectory in 3 dimensions

In cole-trapnell-lab/monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

Plot a dataset and trajectory in 3 dimensions

Description

Plot a dataset and trajectory in 3 dimensions

Usage

plot_cells_3d(
  cds,
  dims = c(1, 2, 3),
  reduction_method = c("UMAP", "tSNE", "PCA", "LSI", "Aligned"),
  color_cells_by = "cluster",
  genes = NULL,
  show_trajectory_graph = TRUE,
  trajectory_graph_color = "black",
  trajectory_graph_segment_size = 5,
  norm_method = c("log", "size_only"),
  color_palette = NULL,
  color_scale = "Viridis",
  cell_size = 25,
  alpha = 1,
  min_expr = 0.1
)

Arguments

cds	cell_data_set to plot
dims	numeric vector that indicates the dimensions used to create the 3D plot, by default it is the first three dimensions.
reduction_method	string indicating the reduction method to plot.
color_cells_by	the cell attribute (e.g. the column of colData(cds)) to map to each cell's color. Default is cluster.
genes	a gene name or gene id to color the plot by.
show_trajectory_graph	a logical used to indicate whether to graph the principal graph backbone. Default is TRUE.
trajectory_graph_color	the color of graph backbone. Default is black.
trajectory_graph_segment_size	numeric indicating the width of the graph backbone. Default is 5.
norm_method	string indicating the method used to transform gene expression when gene markers are provided. Default is "log". "size_only" is also supported.
color_palette	List of colors to pass to plotly for coloring cells by categorical variables. Default is NULL. When NULL, plotly uses default colors.
color_scale	The name of the color scale passed to plotly for coloring cells by numeric scale. Default is "Viridis".
cell_size	numeric indicating the size of the point to be plotted. Default is 25.
alpha	numeric indicating the alpha value of the plotted cells. Default is 1.
min_expr	numeric indicating the minimum marker gene value to be colored. Default is 0.1.

Value

a plotly plot object

Examples

## Not run: 
plot_cells_3d(cds, markers=c("Rbfox3, Neurod1", "Sox2"))

## End(Not run)

cole-trapnell-lab/monocle3 documentation built on June 11, 2025, 11:22 p.m.