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

Description Usage Arguments Value See Also Examples

Description

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

Usage

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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

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## 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)

monocle documentation built on Nov. 8, 2020, 5:06 p.m.