PlotSWNE: Plots swne embedding

Description Usage Arguments Value

View source: R/swne_plotting.R

Description

Plots swne embedding

Usage

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

Arguments

swne.embedding

SWNE embedding (list of factor and sample coordinates) from EmbedSWNE

alpha.plot

Data point transparency

sample.groups

Factor defining sample groups

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