plot_spanning_tree {monocle} | R Documentation

## Plots the minimum spanning tree on cells. This function is deprecated.

### 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)

[Package monocle version 2.12.0 Index]