R/rolePlot.R

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

#' Run Lasso Models
#'
#' 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.
#' @param x A phyloseq object which combined OTU count, taxonomy and metadata
#' @return A matrix of the infile
#' @export

rolePlot <- function(...) {
  if (class(...) =="list" ){
    df_roles <- ...$role
    ggplot(df_roles, aes(participation,connectivity,label=name)) + geom_point(aes(colour = factor(Treatment)))+
      scale_size(guide = 'none')+
      geom_text(aes(label=ifelse(role!="Peripheral",as.character(Order),'')),hjust=0.1,vjust=0.1,size=3,color="black",family="Times New Roman")+
      geom_hline(yintercept=2.5, linetype="dashed", color = "red")+
      geom_vline(xintercept = 0.62, linetype="dashed",color = "blue")+
      annotate("text", x = 0.2, y = 3, label = "Module hubs",color="gray20",size=8,family="Times New Roman")+
      annotate("text", x = 0.75, y = 3, label = " Network hubs",color="gray20",size=8,family="Times New Roman")+
      annotate("text", x = 0.2, y = -2, label = "Peripherals",color="gray20",size=8,family="Times New Roman")+
      annotate("text", x = 0.75, y = -2, label = "Connectors",color="gray20",size=8,family="Times New Roman")+
      labs(x = "Among-module connectivity", y = "Within-module degree", col="Rootstocks") +
      theme_bw() +
      scale_x_continuous(limits = c(0, 1.0))+
      theme(axis.text=element_text(size=16,face="bold",family="Times New Roman"),axis.title=element_text(size=16,face="bold",family="Times New Roman"))+
      labs(fill = "Dose (mg)") +
      theme(legend.title=element_text(size=16,face="bold",family="Times New Roman"),
            legend.text=element_text(size=16,family="Times New Roman")) +
      guides(color = guide_legend(override.aes = list(size=5)))

  } else if (sum(stringr::str_detect(capture.output(str(...)),"role"))> 0 ){

    ggplot(..., aes(participation,connectivity,label=name)) + geom_point(aes(colour = factor(Treatment)))+
      scale_size(guide = 'none')+
      geom_text(aes(label=ifelse(role!="Peripheral",as.character(Order),'')),hjust=0.1,vjust=0.1,size=3,color="black",family="Times New Roman")+
      geom_hline(yintercept=2.5, linetype="dashed", color = "red")+
      geom_vline(xintercept = 0.62, linetype="dashed",color = "blue")+
      annotate("text", x = 0.2, y = 3, label = "Module hubs",color="gray20",size=8,family="Times New Roman")+
      annotate("text", x = 0.75, y = 3, label = " Network hubs",color="gray20",size=8,family="Times New Roman")+
      annotate("text", x = 0.2, y = -2, label = "Peripherals",color="gray20",size=8,family="Times New Roman")+
      annotate("text", x = 0.75, y = -2, label = "Connectors",color="gray20",size=8,family="Times New Roman")+
      labs(x = "Among-module connectivity", y = "Within-module degree", col="Rootstocks") +
      theme_bw() +
      scale_x_continuous(limits = c(0, 1.0))+
      theme(axis.text=element_text(size=16,face="bold",family="Times New Roman"),axis.title=element_text(size=16,face="bold",family="Times New Roman"))+
      labs(fill = "Dose (mg)") +
      theme(legend.title=element_text(size=16,face="bold",family="Times New Roman"),
            legend.text=element_text(size=16,family="Times New Roman")) +
      guides(color = guide_legend(override.aes = list(size=5)))

  } else {

    print("Provide either graph object with list format or data frame")

  }
}