PhONA: Phenotype-OTU based Network Analyses

Introduction

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

# installation 
library(devtools)

## Loading required package: usethis

devtools::install_github("ravinpoudel/PhONA", build_vignettes = TRUE, force = TRUE)

## Downloading GitHub repo ravinpoudel/PhONA@HEAD

## Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
##   download from 'https://api.github.com/repos/ravinpoudel/PhONA/tarball/HEAD' failed

# Browse Vignettes to see the output as below. 
 
browseVignettes("PhONA")

## No vignettes found by browseVignettes("PhONA")

###### 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)

## Assign color to the taxa on the whole phyloseq object so that the same color is assigned for a taxon across treatments
phyobj = taxacolor(phyobj = phyobj, coloredby = "Phylum")

example_lm <- PhONA(
  physeqobj = phyobj,
  cordata = sparcc.cor,
  pdata = sparcc.pval,
  model = "lm",
  iters=1,
  OTU_OTU_pvalue = 0.05,
  OTU_OTU_rvalue = 0.5,
  OTU_Phenotype_pvalue = 0.6,
  definePhenotype = "Marketable",
  defineTreatment = "Maxifort",
  PhenoNodecolor = "yellow",
  PhenoNodesize = 20,
  PhenoNodelabel = "Yield",
  nodesize = 10,
  Pheno2OTUedgecolor = "black",
  netlayout = layout.fruchterman.reingold
)

## Total number of iterations used: 1

Summary of the graph

kable(summarizePhONA(example_lm$phona_graph, example_lm$roles))

node	edge	nodeDegree	avgpath	trans	mod	connectance	wtc	nModules.SA	top3hub	top3hubv	n_postiveL	n_negativeL
235	1019	4.336	1.963	0.773	0.314	0.018	30	6	1;17;36	1;0.578;0.56	496	289

Role analyses using SA algorithm implemented in rnetcarto package.

rolePlot(example_lm)

library(PhONA)
example_lasso <- PhONA(
  physeqobj = phyobj,
  cordata = sparcc.cor,
  pdata = sparcc.pval,
  model = "lasso",
  iters=2,
  OTU_OTU_pvalue = 0.001,
  OTU_OTU_rvalue = 0.6,
  OTU_Phenotype_pvalue = 0.6,
  definePhenotype = "Marketable",
  defineTreatment = "Maxifort",
  PhenoNodecolor = "yellow",
  PhenoNodesize = 20,
  PhenoNodelabel = "Yield",
  nodesize = 10,
  Pheno2OTUedgecolor = "black",
  netlayout = layout.fruchterman.reingold
)

## Total number of iterations used: 2

Summary of the graph

kable(summarizePhONA(example_lasso$phona_graph, example_lasso$roles))

node	edge	nodeDegree	avgpath	trans	mod	connectance	wtc	nModules.SA	top3hub	top3hubv	n_postiveL	n_negativeL
61	181	2.967	3.108	0.601	0.364	0.049	8	7	38;23;24	1;0.932;0.897	107	69

rolePlot(example_lasso)

Ravin Poudel

2021-08-24

Introduction