Various Utilities for Microbial Genomics and Metagenomics

A collection of functions for microbial ecology and other applications of genomics and metagenomics. Companion package for the Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016 ).

enveomics.R

Installing enveomics.R

To install the latest version of enveomics.R uploaded to CRAN, execute in R:

install.packages('enveomics.R')

To install the current developer version of enveomics.R, execute in R:

install.packages('devtools')
library('devtools')
install_github('lmrodriguezr/enveomics', subdir='enveomics.R')

Using enveomics.R

To load enveomics.R, simply execute:

library(enveomics.R);

And open help messages using any of the following commands:

?enveomics.R
?enve.barplot
?enve.recplot2
?enve.recplot2.compareIdentities
?enve.recplot2.changeCutoff
?enve.recplot2.findPeaks
?enve.recplot2.corePeak
?enve.recplot2.windowDepthThreshold
?enve.recplot2.extractWindows
?enve.recplot2.coordinates
?enve.recplot2.seqdepth
?enve.recplot2.ANIr
?enve.prune.dist
?enve.tribs
?enve.tribs.test
?enve.growthcurve
?enve.col.alpha
?enve.truncate

You can run some examples using these libraries in the enveomics-GUI.

For additional information on recruitment plots, see the Recruitment plots working document.

Changelog

• 1.8.0: New functions enve.selvector and enve.prefscore.
• 1.7.1: Improved efficiency of enve.df2dist about five-fold.
• 1.7.0: Uniformized output for enve.recplot2.extractWindows and enve.recplot2.coordinates to ease automation. Thanks to Tomeu Viver and Roth Conrad for troubleshooting.
• 1.6.0: Speed up in recplot2 with proper structure manipulation (by: Kenji Gerhardt). Also, default value for id.breaks was changed from 300 to 60.
• 1.5.0: Modernized documentation, now in ROxygen2 (by: Tatyana Kiryutina)
• 1.4.4: Removes modeest library as requirement, and replaces mower peak-finder initialization to median (instead of mode).
• 1.4.2: Solved bug #36.
• 1.4.0: New option pos.breaks.tsv for enve.recplot2.
• 1.3.4: Gracefully handles and plots recruitment plots with insufficient data to find peaks.
• 1.3.3: New function enve.recplot2.windowDepthThreshold.
• 1.3.2: New option panel.fun for plot.enve.RecPlot2.
• 1.3.1: New function enve.truncate.
• 1.3: Several bug fixes and new utilities for recruitment plots (recplot2).
• 1.1.0: New function enve.growthcurve and related class enve.GrowthCurve with S3 methods plot and summary.
• 1.0.2: Fine-tuned default parameters in enve.recplot2.findPeaks and solved a minor bug in enve.recplot2 that caused failures in low-coverage datasets when using too many threads.
• 1.0.1: enve.recplot2 now supports pos.breaks=0 to define a bin per subject sequence.