CommunityPhyloStru: Community Phylogenetic Structure from 'picante' Package

In walterxie/ComMA: Community Matrix Analysis

Description

A wrapper class using picante Package. Data input t.community.matrix is a transposed matrix from community matrix we defined in ComMA. phylo.tree is a rooted tree of phylo object, which can get from ape read.tree.

Usage

phylo.alpha(t.community.matrix, phylo.tree, include.root = TRUE,
  ORD.RES = function(res) {     res[order(rownames(res)), ] },
  verbose = TRUE)

phylo.mpd(t.community.matrix, phylo.tree, ORD.RES = function(res) {    
  res[order(rownames(res)), ] }, verbose = TRUE)

phylo.mntd(t.community.matrix, phylo.tree, ORD.RES = function(res) {    
  res[order(rownames(res)), ] }, verbose = TRUE)

phylo.beta.dist(t.community.matrix, phylo.tree, verbose = TRUE)

phylo.unifrac.dist(t.community.matrix, phylo.tree, verbose = TRUE)

printResult(pd.alpha = NULL, pd.mpd = NULL, pd.mntd = NULL,
  pd.beta.dist = NULL, filePath, fileStem, tableFile = NULL)

plotPDBeta(pd.beta.dist, title = "Phylogenetic beta diversity", xlab = "",
  sub = "", ...)

Arguments

t.community.matrix	A transposed matrix from community matrix, where rows are samples, columns are OTUs.
phylo.tree	A rooted tree of phylo object
ORD.RES	The function how to order the sample names in the result
verbose	default TRUE
pd.alpha	The result of phylogenetic alpha diversity, ignore it if NULL.
pd.mpd	The result of MPD, ignore it if NULL.
pd.mntd	The result of MNTD, ignore it if NULL.
pd.beta.dist	The result of phylogenetic beta diversity, ignore it if NULL.
filePath	The path to create the file if tableFile is not NULL.
fileStem	The file prefix to identify the result multi-conditions from multi-datasets
tableFile	If NULL, then print the results to console, otherwise print them to the file. Default to NULL.

Details

phylo.alpha returns a data frame of the PD and species richness (SR) values for all samples from pd in picante. Phylogenetic alpha diversity (PD) index is proposed by Faith (1992).

phylo.mpd returns picante ses.mpd, which is MPD standardized effect size of mean pairwise distances in communities. When used with a phylogenetic distance matrix, equivalent to -1 times the Nearest Taxon Index (NTI).

phylo.mntd returns picante ses.mntd, which is MNTD standardized effect size of mean nearest taxon distances in communities.

phylo.beta.dist returns dist object from picante comdist, which is phylogenetic beta diversity (Steven Kembel).

phylo.unifrac.dist calculates unweighted UniFrac and returns dist object from picante unifrac.

printResult prints intermediate data to either file or console.

plotPDBeta plots the dendrogram of phylogenetic beta diversity (Steven Kembel)

Note

If taxa in phylogenies do not match OTUs in the community, then use match.phylo.comm before phylo.alpha. See examples. But prefer comm > phy in practical, otherwise combined$phy will be unrooted tree. Therefore, in the case of single-species samples the PD will be equal to NA (include.root=FALSE), see pd.

Examples

pd.alpha <- phylo.alpha(t.community.matrix, phylo.tree)
pd.alpha
\tabular{rrr}{
   \tab PD \tab SR\cr
  CM30b51 \tab 402.0822 \tab 2796\cr
  CM30b58 \tab 456.4397 \tab 2634\cr
  CM30b60 \tab 554.9873 \tab 2931
}

combined <- match.phylo.comm(phylo.tree, t.communityMatrix)
pd.alpha <- phylo.alpha(combined$comm, combined$phy, ...) 

pd.mpd <- phylo.mpd(t.community.matrix, phylo.tree)

pd.mntd <- phylo.mntd(t.community.matrix, phylo.tree)
pd.beta.dist <- phylo.beta.dist(t.community.matrix, phylo.tree)

unifrac.dist <- phylo.unifrac.dist(t.community.matrix, phylo.tree)

tableFile <- file.path(workingPath, "report.tex")
pdFilePath <- file.path(workingPath, "data", "pd")
mkdir(pdFilePath) 
fileStem <- paste("16S", postfix(taxa.group, isPlot, sep="-"), sep = "-")
printResult(pd.alpha, pd.mpd, pd.mntd, pd.beta.dist, pdFilePath, fileStem, tableFile)

library(pryr);library(gg1L)
p %<a-% plotPDBeta(pd.beta.dist)
gg1L::pdf.plot(p, fig.path="pd-beta.pdf", width=10, height=5)  

walterxie/ComMA documentation built on May 3, 2019, 11:51 p.m.