b5_model.R

b5_model <- function(x, b, c, d, e, f) {
  c+(d-c)/(1+exp(b*(x-e)))^f
}

plot_b5 <- function(listdf, par){
  cycunl = lapply(listdf, function(x) unlist(x$Cycle))
  cycmax <- max(unlist(cycunl)) ; xs = 1:cycmax
  plot(x=xs, y=b5_model(xs, b=par$params$b[1], c=par$params$c[1],
                        d=par$params$d[1], e=par$params$e[1], f=par$params$f[1]), 
                        type="l", xlab="Cycle", ylab="Fluorescence", 
                        ylim=c(range(unlist(listdf)[(names(unlist(listdf))[!grepl("Cycle", 
                                                     names(unlist(listdf)))])])))
    for(k in 2:length(listdf)){
       lines(x=xs, y=b5_model(xs, b=par$params$b[k], c=par$params$c[k],
                              d=par$params$d[k], e=par$params$e[k], 
                              f=par$params$f[k]), col=k)
    for(j in 2:length(listdf[[k]])){
      for(h in 1:length(listdf)){
        points(x=xs, y=listdf[[h]][,j][1:cycmax], cex=0.45)
      }
    }
  }
  legend("topleft", c(LETTERS[1:length(listdf)]), 
         col=1:length(listdf), ncol=2, lty=1, cex=0.5)
}

subplot_b5 <- function(listdf){
  #get fitted models of each replicate within list
  par <- lapply(listdf, function(x) sub_genparams(b5, x)) #KW test results
  #plot the model
  for(i in 1:length(listdf)){
    xs = listdf[[i]]$Cycle
    tryCatch({plot(x=xs, y=b5_model(xs, b=par[[i]]$params$b[1], c=par[[i]]$params$c[1],
                                        d=par[[i]]$params$d[1], e=par[[i]]$params$e[1], 
                                        f=par[[i]]$params$f[1]), type="l",  
         xlab="Cycle", ylab="Fluorescence", 
         ylim=c(range(unlist(listdf[[i]])[(names(unlist(listdf[[i]]))[!grepl("Cycle", 
                                      names(unlist(listdf[[i]])))])])))}, 
         error = function(e){})#xaxt="n", yaxt="n"
    for(k in 2:length(par[[i]]$params)){
      lines(x=xs, y=b5_model(xs, b=par[[i]]$params$b[k], c=par[[i]]$params$c[k],
                                 d=par[[i]]$params$d[k], e=par[[i]]$params$e[k], 
                                 f=par[[i]]$params$f[k]), col=k)
      for(j in 2:length(listdf[[i]])){
        points(x=xs, y=listdf[[i]][,j], cex=0.45, col = j-1)
      }
    }
    legend("topleft", c(names(listdf[[i]])[2:length(listdf[[i]])]), 
           col=1:(length(listdf[[i]])-1), ncol=2, lty=1, cex=0.65)
    #x.intersp=0.25, text.width=c(rep(0,6), rep(0.5,6))
  }
}