MicEco: Various functions for analysis for microbial community data
Installation
library(devtools)
install_github("Russel88/MicEco")
Citation
Phyloseq extensions
ps_prune
Prune taxa (ASVs, OTUs) from a phyloseq object based on their abundance and/or prevalence
ps_venn
Make Venn diagram of shared taxa (ASVs, OTUs) across sample groups from a phyloseq object. Overlap can be weighted by relative abundance
ps_euler
Make Euler diagram of shared taxa (ASVs, OTUs) across sample groups from a phyloseq object. Overlap can be weighted by relative abundance
ps_pheatmap
Make pretty heatmap directly from a phyloseq object. Built-in agglomoration, filtering, ordering, scaling, transformation, and annotation.
rcurve
Rarefaction curve (theoretical and fast) from a phyloseq object. Output ready for plotting in ggplot2
ps_tax_clean
Clean tax_table such that NAs are replaced with names of the most specific known taxonomy prefixed with the rank.
Miscellaneous functions
clr
CLR transformation of community matrix, with multiplicative zero replacement
adonis_OmegaSq
Calculate the unbiased effect size estimation (partial) omega-squared for adonis (PERMANOVA) models
WdS.test
Wd* - robust distance-based multivariate analysis of variance (https://doi.org/10.1186/s40168-019-0659-9). This code is taken from https://github.com/alekseyenko/WdStar/. An alternative to PERMANOVA.
UniFrac.multi
With unrooted phylogenies UniFrac sets the root randomly on the tree. The position of the root affects the results. This function runs UniFrac multiple times in parallel, with different roots, and takes the average to smooth potential bias.
proportionality
Calculate proportionality on a phyloseq object or otu-table. Proposed by Lovell et al. 2016 Proportionality: a valid alternative to correlation for relative data (http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004075)
16S rRNA gene copy number analyses
community_rrna
Calculate the average 16S rRNA copy number of the OTUs in a community/sample
Please cite Schostag et al. 2019 ISMEJ if you use this function.
rarefy_rrna
Combines rarefaction with 16S rRNA copy number correction. It rarefies counts with a probability of the inverse 16S rRNA copy number, such that besides rarefying the read counts the otu-table will be corrected for the varying 16S rRNA copy numbers of the OTUs.
Neutral model
neutral.fit
Fit neutral model developed by Sloan et al. (2006, Environ Microbiol 8(4):732-740) and implemented by Burns et al. (2015, ISME J 10(3):655-664).
neutral.rand
Fit neutral model developed by Sloan et al. (2006, Environ Microbiol 8(4):732-740) and implemented by Burns et al. (2015, ISME J 10(3):655-664) several times on ramdomly picked samples and with 16S rRNA gene copy number corrected rarefaction (rarefy_rrna).
Beta diversity null models
ses.UniFrac
Standardized effect size of UniFrac, based on null models created with permatfull/permatswap from the vegan package, or simple shuffling of phylogenetic tree.
ses.comdist
Standardized effect size of MPD (mean pairwise distance) separating taxa in two communities, a measure of phylogenetic beta diversity (also called betaNRI and betaMPD). This is a combination of ses.mpd (Standardized effect size of MPD in single communities) and comdist (MPD between two communities) from the picante package.
ses.comdistnt
Standardized effect size of MNTD (mean nearest taxon distance) separating taxa in two communities, a measure of phylogenetic beta diversity (also called betaNTI and betaMNTD). This is a combination of ses.mntd (Standardized effect size of MNTD in single communities) and comdistnt (MNTD between two communities) from the picante package.
ses.comdist2
As ses.comdist, but null models are created with permatfull/permatswap
from the vegan package
ses.comdistnt2
As ses.comdistnt, but null models are created with
permatfull/permatswap from the vegan package
comdist.par
A parallel version of the comdist function from the picante package for significant speedup on large datasets
comdistnt.par
A parallel version of the comdistnt function from the picante package for significant speedup on large datasets
ses.mpd.par
A parallel version of the ses.mpd function from the picante package for significant speedup on large datasets
ses.mntd.par
A parallel version of the ses.mntd function from the picante package for significant speedup on large datasets
ses.permtest
Permutation test of z-matrix from ses.comdist, ses.comdist2, ses.comdistnt, ses.comdistnt2 and ses.UniFrac.
Copyright notice
rarefy_rrna: Some code is from vegan licensed under GPL-2
(https://github.com/vegandevs/vegan)
ses.mpd.par, ses.mntd.par, comdist.par, comdistnt.par, ses.comdist, ses.comdist2, ses.comdistnt and ses.comdistnt2: Some
code is from picante licensed under GPL-2
(https://github.com/skembel/picante)