plot_cell_trajectory {monocle} | R Documentation

## Plots the minimum spanning tree on cells.

### Description

Plots the minimum spanning tree on cells.

### Usage

    plot_cell_trajectory(cds, x = 1, y = 2, color_by = "State",
      show_tree = TRUE, show_backbone = TRUE, backbone_color = "black",
      markers = NULL, use_color_gradient = FALSE, markers_linear = FALSE,
      show_cell_names = FALSE, show_state_number = FALSE, cell_size = 1.5,
      cell_link_size = 0.75, cell_name_size = 2, state_number_size = 2.9,
      show_branch_points = TRUE, theta = 0, ...)

### 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
`use_color_gradient` | Whether or not to use color gradient instead of cell size to show marker expression level
`markers_linear` | a boolean used to indicate whether you want to scale the markers logarithimically or linearly
`show_cell_names` | draw the name of each cell in the plot
`show_state_number` | show state number
`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
`state_number_size` | the size of the state number
`show_branch_points` | Whether to show icons for each branch point (only available when reduceDimension was called with DDRTree)
`theta` | How many degrees you want to rotate the trajectory
`...` | Additional arguments passed into scale_color_viridis function

### Value

a ggplot2 plot object

### Examples

    ## Not run:
    lung <- load_lung()
    plot_cell_trajectory(lung)
    plot_cell_trajectory(lung, color_by="Pseudotime", show_backbone=FALSE)
    plot_cell_trajectory(lung, markers="MYH3")

    ## End(Not run)

[Package monocle version 2.12.0 Index]