plotDot: Dot Plot

In farrellja/URD: URD

Description

importFrom reshape2 melt

Usage

plotDot(
  object,
  genes,
  clustering,
  clusters.use = NULL,
  min.exp = 0.05,
  size.min = 0,
  size.max = 5,
  scale.by = c("radius", "area"),
  colors = NULL,
  mean.expressing.only = F,
  title = ""
)

Arguments

object	An URD object
genes	(Character Vector) Genes to plot
clustering	(Character) Name of clustering to use (i.e. a column name of @group.ids)
clusters.use	(Character vector) Names of specific clusters to plot (default: all clusters)
min.exp	(Numeric) Minimum proportion of expressing cells (0-1) to be shown on the plot
size.min	(Numeric) Point size for clusters with no cells expressing
size.max	(Numeric) Point size for clusters with all cells expressing
scale.by	(Character) Should point size scale by radius or area? See scale_radius and scale_size.
colors	(Character vector) Vector of colors to use for a palette.
mean.expressing.only	(Logical) Should mean expression value exclude cells with no expression
title	(Character) How should the plot be titled? (Default: no title)

Value

A ggplot2 object

farrellja/URD documentation built on June 17, 2020, 4:48 a.m.