plot_complex_cell_trajectory {monocle}R Documentation

Plots the minimum spanning tree on cells.

Description

Plots the minimum spanning tree on cells.

Usage

plot_complex_cell_trajectory(
  cds,
  x = 1,
  y = 2,
  root_states = NULL,
  color_by = "State",
  show_tree = TRUE,
  show_backbone = TRUE,
  backbone_color = "black",
  markers = NULL,
  show_cell_names = FALSE,
  cell_size = 1.5,
  cell_link_size = 0.75,
  cell_name_size = 2,
  show_branch_points = TRUE,
  ...
)

Arguments

cds

CellDataSet for the experiment

x

the column of reducedDimS(cds) to plot on the horizontal axis

y

the column of reducedDimS(cds) to plot on the vertical axis

root_states

the state used to set as the root of the graph

color_by

the cell attribute (e.g. the column of pData(cds)) to map to each cell's color

show_tree

whether to show the links between cells connected in the minimum spanning tree

show_backbone

whether to show the diameter path of the MST used to order the cells

backbone_color

the color used to render the backbone.

markers

a gene name or gene id to use for setting the size of each cell in the plot

show_cell_names

draw the name of each cell in the plot

cell_size

The size of the point for each cell

cell_link_size

The size of the line segments connecting cells (when used with ICA) or the principal graph (when used with DDRTree)

cell_name_size

the size of cell name labels

show_branch_points

Whether to show icons for each branch point (only available when reduceDimension was called with DDRTree)

...

Additional arguments passed to the scale_color_viridis function

Value

a ggplot2 plot object

Examples

## Not run: 
library(HSMMSingleCell)
HSMM <- load_HSMM()
plot_complex_cell_trajectory(HSMM)
plot_complex_cell_trajectory(HSMM, color_by="Pseudotime", show_backbone=FALSE)
plot_complex_cell_trajectory(HSMM, markers="MYH3")

## End(Not run)

[Package monocle version 2.21.1 Index]