monocle (version 1.6.2)

plot_spanning_tree: Plots the minimum spanning tree on cells.

Description

Plots the minimum spanning tree on cells.

Usage

plot_spanning_tree(cds, x = 1, y = 2, color_by = "State",
  show_tree = TRUE, show_backbone = TRUE, backbone_color = "black",
  markers = NULL, show_cell_names = FALSE, cell_name_size = 1)

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

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_name_size

the size of cell name labels

Value

• a ggplot2 plot object

Examples

data(HSMM)
plot_spanning_tree(HSMM)
plot_spanning_tree(HSMM, color_by="Pseudotime", show_backbone=FALSE)
plot_spanning_tree(HSMM, markers="MYH3")