FeaturePlotSWNE: Plots swne embedding with feature overlayed

Description Usage Arguments Value

View source: R/swne_plotting.R

Description

Plots swne embedding with feature overlayed

Usage

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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 Dec. 7, 2018, 8:55 a.m.