lefserPlot: Plots results from 'lefser' function

In waldronlab/lefser: R implementation of the LEfSE method for microbiome biomarker discovery

Plots results from lefser function

Description

This function plots the biomarkers found by LEfSe, that are ranked according to their effect sizes and linked to their abundance in each class.

Usage

lefserPlot(
  df,
  colors = "c",
  trim.names = TRUE,
  title = "",
  label.font.size = 3
)

Arguments

df	Data frame produced by lefser. This data frame contains two columns labeled as c("features", "scores").
colors	Colors corresponding to class 0 and 1. Options: "c" (colorblind), "l" (lefse), "g" (greyscale). Defaults to "c". This argument also accepts a character(2) with two color names.
trim.names	Under the default (TRUE), this function extracts the most specific taxonomic rank of organism.
title	A character(1). The title of the plot.
label.font.size	A numeric(1). The font size of the feature labels. The default is 3.

Value

Function returns plot of effect size scores produced by lefser. Positive scores represent the biomarker is more abundant in class '1'. Negative scores represent the biomarker is more abundant in class '0'.

Examples

example("lefser")
lefserPlot(res_class)

waldronlab/lefser documentation built on Nov. 1, 2024, 9:02 p.m.