R/plotMonoExp.R

In ppernot/FitOCTlib: Stan-based functions to fit OCT signals

#  plotMonoExp.R
#' Plot outputs from \code{fitMonoExp}.
#' 
#' @param x a numeric vector
#' @param y a numeric vector of responses/data
#' @param uy a numeric vector of uncertainties
#' @param ySmooth a numeric vector of smoothed data
#' @param mod a numeric vector of model values
#' @param resid a numeric vector of residuals
#' @param gPars a list of graphical parameters and colors
#' @param dataType an numeric (1 or 2) defining the type of data 
#' @param br a list output from \code{printBr()}
#' 
#' @return Produces a plot.
#' 
#' @author Pascal PERNOT
#' 
#' @export

plotMonoExp <- function(x, y, uy, ySmooth, 
                        mod, resid, gPars, 
                        dataType, br) {
  
  # Extract graphical parameters
  for (n in names(gPars))
    assign(n,rlist::list.extract(gPars,n))
  
  par(mfrow=c(1,2), pty=pty, mar=mar, mgp=mgp, tcl=tcl, lwd=lwd, cex=cex)
  
  if (dataType==1)
    ylabel = "mean amplitude (a.u.)"
  if (dataType==2)
    ylabel = "mean intensity (a.u.)"
  
  # Fit
  plot(x,y,pch=20,cex=0.5,col=cols[6],
       main= plot_title,
       xlab= xlabel,
       ylab= ylabel)
  grid()
  lines(x,mod,col=cols[7])
  legend('topright', bty='n', cex=cex.leg,
         title = '', title.adj = 1,
         legend=c('data','best fit'),
         pch=c(20,NA),lty=c(-1,1),
         col=c(cols[6],cols[7])
  )
  legend('topright', bty='n', cex=cex.leg,
         legend=c('','','','',
                  as.expression(
                    bquote(
                      "br    " == .(formatC(br$br,digits=3)))
                    ),
                  as.expression(
                    bquote(
                      "CI95" == .(paste0(signif(br$CI95,2),collapse='-')))
                    )
         )
  )
  box()
  
  # Residus
  ylim=1.2*max(abs(resid))*c(-1,1)
  res = resid
  plot(x,res,type='n',
       main ='Residuals',
       xlab = xlabel,
       ylim = ylim, 
       ylab ='residuals (a.u.)')
  grid()
  abline(h=0)
  polygon(c(x,rev(x)),c(-2*uy,rev(2*uy)),col=col_tr2[4],border = NA)
  points(x,res,pch=20,cex=0.75,col=cols[6])
  lines(x, ySmooth-mod, col=cols[7])
  legend('topright', bty='n', cex=cex.leg,
         title = '', title.adj = 1,
         legend=c('mean resid.','data 95% uncert.','best fit - smooth'),
         pch=c(20,NA,NA),lty=c(-1,1,1),lwd=c(lwd,10,lwd),
         col=c(cols[6],col_tr2[4],cols[7])
  )
  box()
}