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 2.22.0 Index]