compareDistribs: Compare the distribution of a taxon across two groups

In hallucigenia-sparsa/seqgroup: Analysis of Sequencing Data with Groups

Compare the distribution of a taxon across two groups

Description

Plot taxon abundances as histograms and calculate the unpaired two-sided Wilcoxon p-value.

Usage

compareDistribs(
  x,
  taxon,
  groups = c(),
  group1 = 1,
  group2 = 2,
  name1 = as.character(group1),
  name2 = as.character(group2)
)

Arguments

x	a matrix with taxa as rows and samples as columns
taxon	the index or name of a taxon to be compared
groups	a vector that provides for each sample its group membership (numeric or character)
group1	the identifier of the first group (numeric or character)
group2	the identifier of the second group (numeric or character)
name1	the name to be displayed for the first group
name2	the name to be displayed for the second group

Examples

data("ibd_taxa")
data("ibd_metadata")
groups=as.vector(ibd_metadata$Diagnosis)
taxon="Faecalibacterium_prausnitzii"
compareDistribs(ibd_taxa,taxon=taxon,groups=groups,group1="UC",group2="Control")
groups[groups=="UC"]="IBD"
groups[groups=="CD"]="IBD"
# Faecalibacterium has a significantly higher relative abundance in the control group
compareDistribs(ibd_taxa,taxon=taxon,groups=groups,group1="IBD",group2="Control")

hallucigenia-sparsa/seqgroup documentation built on July 6, 2022, 1:11 p.m.