PlotSWNE: Plots swne embedding

In yanwu2014/swne: Similarity Weighted Nonnegative Embedding: A method for visualizing high dimensional datasets

Plots swne embedding

Description

Plots swne embedding

Usage

PlotSWNE(
  swne.embedding,
  sample.groups,
  alpha.plot = 0.25,
  do.label = F,
  label.size = 4.5,
  pt.size = 1,
  samples.plot = NULL,
  show.legend = T,
  seed = NULL,
  colors.use = NULL,
  use.brewer.pal = F,
  contour.geom = "path",
  contour.alpha = 0.25
)

Arguments

swne.embedding	SWNE embedding (list of factor and sample coordinates) from EmbedSWNE
sample.groups	Factor defining sample groups
alpha.plot	Data point transparency
do.label	Label the sample groups
label.size	Label font size
pt.size	Sample point size
samples.plot	Vector of samples to plot. Default is NULL, which plots all samples
show.legend	If sample groups defined, show legend
seed	Seed for sample groups color reproducibility
colors.use	Vector of hex colors for each sample group. Vector names must align with sample.groups
use.brewer.pal	Use RColorBrewer 'Paired' palette instead of default ggplot2 color wheel
contour.geom	Plot contour as either a line or a filled in region
contour.alpha	Transparency of the contour line/region

Value

ggplot2 object with swne plot

yanwu2014/swne documentation built on Aug. 5, 2023, 4:42 a.m.