vignettes/PhONA.md

In ravinpoudel/PhONA: PhONA provides a framework to select a testable and manageable number of OTUs/ASVs to support microbiome-based agriculture

Introduction

PhONA provides a framework to select a testable and manageable number of OTUs to support microbiome-based agriculture

###### Load the data
phyobj <- readRDS(system.file("extdata", "physeqobject.rds", package = "PhONA"))
sparcc.cor <- read.delim(system.file("extdata", "cor_sparcc.out", package = "PhONA"), sep = "\t", header = T, row.names = 1)
sparcc.pval <- read.delim(system.file("extdata", "pvals.txt", package = "PhONA"), sep = "\t", header = T, row.names = 1)

library(PhONA)
PhONA(
  physeqobj = phyobj,
  cordata = sparcc.cor,
  pdata = sparcc.pval,
  model = "lm",
  OTU_OTU_pvalue = 0.001,
  OTU_OTU_rvalue = 0.6,
  OTU_Phenotype_pvalue = 0.6,
  definePhenotype = "Marketable",
  defineTreatment = "Maxifort",
  coloredby = "Phylum",
  PhenoNodecolor = "yellow",
  PhenoNodesize = 20,
  PhenoNodelabel = "Yield",
  nodesize = 10,
  Pheno2OTUedgecolor = "black",
  netlayout = layout.fruchterman.reingold
)

## IGRAPH e3b2317 UN-- 97 299 -- 
## + attr: Kingdom (v/c), Phylum (v/c), Class (v/c), Order (v/c), Family (v/c), Genus (v/c), Species (v/c), color (v/c), name
## | (v/c), size (v/n), nName (v/c), vertex.label.size (v/n), vertex.label_type (v/n), relation (e/c), pv (e/c), weight_1 (e/n),
## | weight_2 (e/n), color_1 (e/c), color_2 (e/c), lty_1 (e/n), lty_2 (e/n), color (e/c), lty (e/n)
## + edges from e3b2317 (vertex names):
##  [1] Otu00663--Otu00681 Otu00327--Otu00377 Otu00272--Otu00315 Otu00270--Otu00521 Otu00234--Otu00435 Otu00231--Otu00529 Otu00231--Otu00327
##  [8] Otu00208--Otu00224 Otu00200--Otu00280 Otu00199--Otu00521 Otu00199--Otu00272 Otu00199--Otu00270 Otu00199--Otu00264 Otu00199--Otu00255
## [15] Otu00190--Otu00345 Otu00185--Otu00250 Otu00170--Otu00379 Otu00170--Otu00213 Otu00161--Otu00876 Otu00157--Otu00264 Otu00155--Otu00270
## [22] Otu00155--Otu00199 Otu00143--Otu00653 Otu00143--Otu00631 Otu00143--Otu00379 Otu00143--Otu00280 Otu00143--Otu00270 Otu00143--Otu00264
## [29] Otu00143--Otu00262 Otu00143--Otu00200 Otu00143--Otu00199 Otu00143--Otu00174 Otu00143--Otu00170 Otu00143--Otu00155 Otu00136--Otu00217
## [36] Otu00135--Otu00202 Otu00126--Otu00656 Otu00125--Otu00280 Otu00125--Otu00270 Otu00125--Otu00264 Otu00125--Otu00262 Otu00125--Otu00199
## + ... omitted several edges

library(PhONA)
PhONA(
  physeqobj = phyobj,
  cordata = sparcc.cor,
  pdata = sparcc.pval,
  model = "lasso",
  OTU_OTU_pvalue = 0.001,
  OTU_OTU_rvalue = 0.6,
  OTU_Phenotype_pvalue = 0.6,
  definePhenotype = "Marketable",
  defineTreatment = "Maxifort",
  coloredby = "Phylum",
  PhenoNodecolor = "yellow",
  PhenoNodesize = 20,
  PhenoNodelabel = "Yield",
  nodesize = 10,
  Pheno2OTUedgecolor = "black",
  netlayout = layout.fruchterman.reingold
)

## + Fold01: alpha=1, lambda=1 
## - Fold01: alpha=1, lambda=1 
## + Fold02: alpha=1, lambda=1 
## - Fold02: alpha=1, lambda=1 
## + Fold03: alpha=1, lambda=1 
## - Fold03: alpha=1, lambda=1 
## + Fold04: alpha=1, lambda=1 
## - Fold04: alpha=1, lambda=1 
## + Fold05: alpha=1, lambda=1 
## - Fold05: alpha=1, lambda=1 
## + Fold06: alpha=1, lambda=1 
## - Fold06: alpha=1, lambda=1 
## + Fold07: alpha=1, lambda=1 
## - Fold07: alpha=1, lambda=1 
## + Fold08: alpha=1, lambda=1 
## - Fold08: alpha=1, lambda=1 
## + Fold09: alpha=1, lambda=1 
## - Fold09: alpha=1, lambda=1 
## + Fold10: alpha=1, lambda=1 
## - Fold10: alpha=1, lambda=1 
## Aggregating results
## Selecting tuning parameters
## Fitting alpha = 1, lambda = 0.727 on full training set

## Waiting for profiling to be done...

## IGRAPH 1f41e22 UN-- 61 182 -- 
## + attr: Kingdom (v/c), Phylum (v/c), Class (v/c), Order (v/c), Family (v/c), Genus (v/c), Species (v/c), color (v/c), name
## | (v/c), size (v/n), nName (v/c), vertex.label.size (v/n), vertex.label_type (v/n), relation (e/n), pv (e/n), weight_1 (e/n),
## | weight_2 (e/n), color_1 (e/c), color_2 (e/c), lty_1 (e/n), lty_2 (e/n), color (e/c), lty (e/n)
## + edges from 1f41e22 (vertex names):
##  [1] Otu00272--Otu00315 Otu00270--Otu00521 Otu00231--Otu00327 Otu00200--Otu00280 Otu00199--Otu00521 Otu00199--Otu00272 Otu00199--Otu00270
##  [8] Otu00199--Otu00264 Otu00170--Otu00379 Otu00157--Otu00264 Otu00155--Otu00270 Otu00155--Otu00199 Otu00143--Otu00379 Otu00143--Otu00280
## [15] Otu00143--Otu00270 Otu00143--Otu00264 Otu00143--Otu00262 Otu00143--Otu00200 Otu00143--Otu00199 Otu00143--Otu00174 Otu00143--Otu00170
## [22] Otu00143--Otu00155 Otu00125--Otu00280 Otu00125--Otu00270 Otu00125--Otu00264 Otu00125--Otu00262 Otu00125--Otu00199 Otu00125--Otu00143
## [29] Otu00109--Otu00167 Otu00109--Otu00161 Otu00108--Otu00167 Otu00108--Otu00109 Otu00095--Otu00379 Otu00095--Otu00170 Otu00095--Otu00143
## [36] Otu00076--Otu00125 Otu00063--Otu00270 Otu00063--Otu00264 Otu00063--Otu00161 Otu00063--Otu00155 Otu00063--Otu00143 Otu00063--Otu00109
## + ... omitted several edges

ravinpoudel/PhONA documentation built on Jan. 30, 2023, 5:12 p.m.