VscAIplot: VscAI visualize the genes, loci and factors that separate...

In sqjin/scAI: integrative analysis of single-cell transcriptomic and epigenomic profiles

Description

VscAI visualize the genes, loci and factors that separate cell states on two dimensions alongside the cells

Usage

VscAIplot(object, gene.use, loci.use, loci.use.names, color.by,
  labels.order = NULL, colors.use = NULL, brewer.use = FALSE,
  xlabel = "VscAI1", ylabel = "VscAI2", title = NULL,
  label.size = 3, cell.size = 0.3, font.size = 10, do.label = T,
  show.legend = T, show.axes = T)

Arguments

object	scAI object
gene.use	embedded genes
loci.use	embedded loci
loci.use.names	alternative names of embedded loci, e.g, the corresponding motif
color.by	the name of the variable in pData, defining cell groups, cells are colored based on the labels
labels.order	defining the factor level
colors.use	defining the color for each cell group
brewer.use	use RColorBrewer palette instead of default ggplot2 color
xlabel	label of x-axis
ylabel	label of y-axis
title	main title of the plot
label.size	font size of the legend
cell.size	size of the dots
font.size	size of font
do.label	label the cluster in 2D space
show.legend	whether show the legend
show.axes	whether show the axes

Value

ggplot2 object with 2D plot

sqjin/scAI documentation built on Nov. 19, 2020, 4:04 p.m.