package-deprecated: Plots the minimum spanning tree on cells. This function is...

In cole-trapnell-lab/monocle-release: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

This function arranges all of the cells in the cds in a tree and predicts their location based on their pseudotime value

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_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
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)

Value

a ggplot2 plot object

See Also

plot_cell_trajectory

Examples

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

## End(Not run)

cole-trapnell-lab/monocle-release documentation built on May 13, 2019, 8:50 p.m.