plotLDA: plot LEfSe results from ldamarker function

In guokai8/microbial: Do 16s Data Analysis and Generate Figures

plot LEfSe results from ldamarker function

Description

plot LEfSe results from ldamarker function

Usage

plotLDA(
  x,
  group,
  lda = 2,
  pvalue = 0.05,
  padj = NULL,
  color = NULL,
  fontsize.x = 4,
  fontsize.y = 5
)

Arguments

x	LEfse results from ldamarker
group	a vector include two character to show the group comparsion
lda	LDA threshold for significant biomarker
pvalue	pvalue threshold for significant results
padj	adjust p value threshold for significant results
color	A vector of character use specifying the color
fontsize.x	the size of x axis label
fontsize.y	the size of y axis label

Value

ggplot2 object

Author(s)

Kai Guo

Examples

data("Physeq")
res <- ldamarker(physeq,group="group")
plotLDA(res,group=c("A","B"),lda=5,pvalue=0.05)

guokai8/microbial documentation built on Oct. 15, 2024, 11:32 p.m.