plotBeta: Plot beta diversity

In microbiomeExplorer: Microbiome Exploration App

Description

This functions plots the beta diversity as a PCoA plot.

Usage

plotBeta(
  aggdat,
  dim = c(1, 2),
  log = TRUE,
  dist_method = "bray",
  pcas = NULL,
  nfeatures = nrow(aggdat),
  col_by = NULL,
  shape_by = NULL,
  plotTitle = "",
  xlab = NULL,
  ylab = NULL,
  pt_size = 8,
  plotText = NULL,
  confInterval = NULL,
  allowWebGL = TRUE,
  pwidth = 550,
  pheight = 550
)

Arguments

aggdat	aggregated MRExperiment
dim	Vector of length 2 specifying which dimensions to plot.
log	Log2 transform data. Default is TRUE.
dist_method	Which distance method to use. See ?vegan::vegdist for more vegdist() for options. Default is "bray".
pcas	precalculated pcas to avoid recalculation via CalcPCs
nfeatures	Number of top features in terms of standard deviation. Default is all.
col_by	Phenotype for coloring.
shape_by	Phenotype for shape.
plotTitle	Plot title. By default, becomes PCoA (codedist.method).
xlab	X-axis label. By default, shows dimension and percent variance explained.
ylab	Y-axis label. By default, shows dimension and percent variance explained.
pt_size	the size of the markers
plotText	adonis text to be added to plot
confInterval	numeric value indicating confidence level for ellipses
allowWebGL	boolean indicating if WebGL should be used
pwidth	overall plot width; default is 550 (125 are added for legend)
pheight	overall plot height; default is 550

Value

plotly plot object

Examples

data("mouseData", package = "metagenomeSeq")
aggdat <- aggFeatures(mouseData, level = "genus")
plotBeta(aggdat)

microbiomeExplorer documentation built on Nov. 8, 2020, 8:16 p.m.