plotUnivar: Plot box-plots of univariate analysis

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Plot box-plots of univariate analysis

Description

Plot box-plots of univariate analysis

Usage

plotUnivar(
  dataset = NULL,
  jitter = T,
  dotplot = F,
  violin = F,
  showStats = T,
  raw = F,
  factor = NULL,
  stratify = F,
  facet.x = NULL,
  facet.y = NULL,
  flattenFactors = F,
  rank = NULL,
  ftlist = NULL,
  unique_groups = NULL,
  plotAll = F,
  alpha = 0.05,
  param = F,
  width = 7,
  height = 6,
  scalePlot = F,
  add_xaxis = F,
  separateLegend = F
)

Arguments

dataset	MicroVis dataset. Defaults to the active dataset
jitter	Show "jitter" points for each sample? Defaults to TRUE
dotplot	Create dotplot? Defaults to FALSE
violin	Create violinplot? Defaults to FALSE
showStats	Show bars w/asterisks for significance labels? Defaults to TRUE
raw	Show raw abundance values? Defaults to FALSE. If TRUE, showStats is forced to FALSE
factor	Factor along which to analyze data
stratify	Stratify the data along a second factor? Defaults to FALSE
facet.x	(Optional) Name of a factor to stratify horizontally
facet.y	(Optional) Name of a factor to stratify vertically
flattenFactors	(Not ready) Combine two factors into one
rank	Rank at which to select features
ftlist	List of specific features to plot. Defaults to all features at the given rank
unique_groups	(Optional) Only plot features that are uniquely over/under- expressed in these groups
plotAll	Plot all features regardless of significance? Defaults to FALSE
alpha	Significance threshold. Defaults to 0.05
param	Perform parametrized analysis? Defaults to FALSE (non-parametrized analysis by default)
width	Width of plot when saved, in inches. Increasing width and height will make text relatively smaller
height	Height of plot when saved, in inches. Increasing width and height will make text relatively smaller
scalePlot	Scale plot by log2? Defaults to FALSE
add_xaxis	Add group labels to the x-axis? Defaults to FALSE
separateLegend	Make one separate figure of just the legend instead of including it in all the boxplots? Defaults to FALSE

Value

MicroVis dataset

microresearcher/MicroVis documentation built on Feb. 8, 2024, 10:59 a.m.