plotLEFSE: Plot LEfSe analysis (not cladogram plot)

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Plot LEfSe analysis (not cladogram plot)

Description

Plot LEfSe analysis (not cladogram plot)

Usage

plotLEFSE(
  dataset = NULL,
  factor = NULL,
  alpha = 0.05,
  lda_cutoff = 2,
  top = 20,
  byrank = F
)

Arguments

dataset	MicroVis dataset. Defaults to the active dataset
factor	Factor to analyze data by. Defaults to the active factor
alpha	Significance threshold. Defaults to 0.05
lda_cutoff	Effect size cutoff for features to plot. Defaults to 2
top	Top number of features by effect size to plot. Defaults to 20
byrank	Facet plot by rank? Defaults to FALSE

Value

Plot of effect sizes of significant features from LEfSe analysis

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