my_plot_cell_clusters: Plots clusters of cells .

In efheuston/MyPlotTrajectoryPackage:

Description

Plots clusters of cells .

Usage

my_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, point_colors = c("#cb4bbe", "lightskyblue", "grey37",
  "#53ba48", "moccasin", "#dcca44", "#502d70", "#afd671", "#cb4471", "#69da99",
  "#d44732", "#6fd3cf", "#5d2539", "#cfd0a0", "blue", "#d2883b", "#6793c0",
  "#898938", "#c98ac2", "yellow", "#c4c0cc", "#7d3d23", "#00a5ff", "#d68d7a",
  "#a2c1a3"), ...)

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)

efheuston/MyPlotTrajectoryPackage documentation built on May 26, 2019, 12:31 p.m.