PhONA: Run PhONA

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

Run PhONA

Description

This function takes in phyloseq object, association matix, p value matrix and create a combined OTU-OTU and OTU-Phenotype network. User can select model to define OTU-Phontype assocaition.

Usage

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

Arguments

physeqobj	A phyloseq object which combined OTU count, taxonomy and metadata
cordata	A pairwise square matrix defining OTU-OTU association
pdata	A pairwise square matrix defining p-value for OTU-OTU association
model	Model to define association between OTUs and Phenotype. Option available are "lm", "lasso". In lasso option, we are using lasso model to reduce the number of features/OTUs. OTUs important to phenotype prediction were ranked using varImp. Selected OTUs were then for reduced GLM model. @iters Number of times a pheotype-otu model to run. Default is 1
OTU_OTU_pvalue	Pvalue for OTU-OTU association
OTU_OTU_rvalue	Level of OTU-OTU association
OTU_Phenotype_pvalue	Pvalue for OTU-Phenotype association
definePhenotype	Phenotype to be used. It is a column header from phenotype data
defineTreatment	Select the treatment. It is same as the treatment name that the phyloseq object represents
PhenoNodecolor	Select color for phenotype node
PhenoNodesize	Select node size for phenotype node
nodesize	Select size for nodes other than phenotype node
Pheno2OTUedgecolor	Select color of edge from OTU to phenotype node
netlayout	Select layout for the network graph. All the layout options from igraph can be used
coloredby	Select taxonomic group to be used for coloring node. Options: Kingdom,Phylum, Class, Order, Family, Genus, Species

Value

A PhONA representing OTU-OTU association as well as OTU-Phenotype association

Examples

Running linear model based PhONA,where OTU-Phenotype association is defined using linear model
PhONA(
physeqobj = phyobj,
cordata = sparcc.cor,
pdata = sparcc.pval,
model = "lm",
iters = 1,
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)


Running lasso model based PhONA,where OTU-Phenotypeassociation is defined using lasso model and GLM

PhONA(
physeqobj = phyobj,
cordata = sparcc.cor,
pdata = sparcc.pval,
model = "lasso",
iters = 1,
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)

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