FeaturePlotSWNE: Plots swne embedding with feature overlayed

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

Plots swne embedding with feature overlayed

Description

Plots swne embedding with feature overlayed

Usage

FeaturePlotSWNE(
  swne.embedding,
  feature.scores,
  feature.name = NULL,
  alpha.plot = 0.5,
  quantiles = c(0.01, 0.99),
  samples.plot = NULL,
  label.size = 4.5,
  pt.size = 1,
  color.palette = "YlOrRd",
  contour.geom = "path",
  contour.alpha = 0.25
)

Arguments

swne.embedding	SWNE embedding (list of NMF and sample coordinates) from EmbedSWNE
feature.name	Name of feature to overlay
alpha.plot	Data point transparency
quantiles	Quantiles to trim outliers from
samples.plot	Samples to actually plot. Default is NULL, which plots all samples
label.size	Label font size
pt.size	Sample point size
color.palette	RColorbrewer palette to use
contour.geom	Plot contour as either a line or a filled in region
contour.alpha	Transparency of the contour line/region
feature.score	Feature vector to overlay

Value

ggplot2 object with swne plot with feature overlayed

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