PhONA.RdThis 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.
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 )
| 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 |
| 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 |
A PhONA representing OTU-OTU association as well as OTU-Phenotype association
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)#> Error in 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): unused argument (coloredby = "Phylum")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)#> Error in 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): unused argument (coloredby = "Phylum")