compareGroups: Compare diversity-related properties across groups

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

Compare diversity-related properties across groups

Description

The function allows to compare richness, evenness, alpha diversity and beta diversity across groups, where beta diversity can be assessed with both a Bray Curtis distribution or overdispersion from a Dirichlet-Multinomial distribution fit. By default, groups are subsampled to the same sample number, for this reason the output of the same run can differ. To switch off this behaviour, subsample can be set to false. Chao1 and Shannon diversity are computed with vegan. The Taylor law is computed taxon-wise as the slope of the regression line for the logarithm of the mean abundance of taxa and the logarithm of the variance of taxa.

Usage

compareGroups(
  abundances,
  property = "beta",
  method = "dissim",
  groups = c(),
  colors = c(),
  colorMap = NULL,
  plot.type = "pergroup",
  avg = "none",
  all = FALSE,
  noSameGroup = TRUE,
  rowNorm = FALSE,
  subsample = TRUE,
  xlab = "",
  pvalViz = FALSE,
  pAdjMethod = "BH",
  returnValues = FALSE
)

Arguments

abundances	a matrix with taxa as rows and samples as columns
property	richness (Chao1), evenness (Sheldon), alpha (alpha-diversity with Shannon index), beta (beta-diversity), taylor (slope of the Taylor law)
method	for beta-diversity, dissim (Bray Curtis dissimilarities) and DM (estimation of theta with package dirmult) are supported
groups	group membership vector with as many entries as samples in abundances
colors	optional color vector with as many entries as (unique) groups (only for plot.type pergroup)
colorMap	optional color map with a color for a metadata value, required for color legend (only for plot.type pergroup)
plot.type	pergroup (plot property per group; this is the only plot type available for richness, evenness, alpha and beta with DM) and intravsinter (plot property for all within-group samples versus all samples)
avg	none, mean or median (average group property with the selected averaging method, does not work for method DM)
all	include the beta diversity for all samples
noSameGroup	for beta diversity with method dissim: only between-group pairs are used to calculate the beta diversity for all samples
rowNorm	for beta diversity with method dissim: normalize the abundances row-wise
subsample	subsample groups randomly to have the same sample number in each group; for plot type intravsinter, it equalises in additon the number of pairs within and between groups
xlab	the x axis label
pvalViz	if true and avg is set to none and plot.type is pergroup, Wilcoxon p-values are displayed on the violin plot using function stat_compare_means in R package ggpubr
pAdjMethod	multiple testing correction method to use for p-value plotting (values are those accepted by p.adjust)
returnValues	if true, return properties

Value

if returnValues is true, properties are returned

Examples

data("ibd_taxa")
data("ibd_metadata")
groups=as.vector(ibd_metadata$Diagnosis)
compareGroups(ibd_taxa,groups=groups,property="alpha",pvalViz = TRUE)
data("floresgut_taxa")
data("floresgut_metadata")
groups=floresgut_metadata$host_subject_id
diet.col=makeColorsGivenMetadata(metadataItem=floresgut_metadata$diet,groups=groups)
compareGroups(floresgut_taxa,groups=groups,colors=diet.col$colors,colorMap=diet.col$colormap)
age=floresgut_metadata$age
age.col=makeColorsGivenMetadata(metadataItem=age,groups=groups,binning="equaldist",numBins=10)
col=age.col$colors
compareGroups(floresgut_taxa,groups=groups,property="alpha",colors=col,colorMap=age.col$colormap)

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