plot_cell_clusters: Plots clusters of cells .

In monocle: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

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)

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