PlotDims: Plots 2D embedding

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

Plots 2D embedding

Description

Plots 2D embedding

Usage

PlotDims(
  dim.scores,
  sample.groups,
  x.lab = "tsne1",
  y.lab = "tsne2",
  main.title = NULL,
  pt.size = 1,
  font.size = 12,
  alpha.plot = 1,
  do.label = T,
  label.size = 4,
  show.legend = T,
  show.axes = T,
  seed = NULL,
  colors.use = NULL,
  use.brewer.pal = F
)

Arguments

dim.scores	2D embedding coordinates. Must be N x 2 samples
sample.groups	Factor defining sample groups
x.lab	X axis label
y.lab	Y axis label
main.title	Main plot title
pt.size	Sample point size
font.size	Font size for axis labels
alpha.plot	Data point transparency
do.label	Label the sample groups
label.size	Label font size
show.legend	If sample groups defined, show legend
show.axes	Plot x and y axes
seed	Seed for sample group 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

Value

ggplot2 object with 2d plot

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