plot_cell_clusters {monocle} | R Documentation

## Plots clusters of cells .

### Description

Plots clusters of cells .

### Usage

    plot_cell_clusters(cds, x = 1, y = 2, color_by = "Cluster",
      markers = NULL, show_cell_names = FALSE, cell_size = 1.5,
      cell_name_size = 2, ...)

### 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
`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_name_size` | the size of cell name labels
`...` | additional arguments passed into the scale_color_viridis function

### Value

a ggplot2 plot object

### Examples

    ## Not run:
    library(HSMMSingleCell)
    HSMM <- load_HSMM()
    HSMM <- reduceD
    plot_cell_clusters(HSMM)
    plot_cell_clusters(HSMM, color_by="Pseudotime")
    plot_cell_clusters(HSMM, markers="MYH3")

    ## End(Not run)

[Package monocle version 2.18.0 Index]