R/PlotsGeneric.R

In kevin-allen/relectro: Analysis of electrophysiological data

#' Plot a boxplot with 2 factors
#'
#' Just a wrapper around boxplot function.
#' To set which level is plot first, consider using the function factor and set the argument levels.
#'
#' @param data data.frame with the data
#' @param dv Dependent variable. The one you want on the y-axis
#' @param iv1 First independent variable
#' @param iv2 Second independent variable
#' @param colors Colors of the bars of the boxplot
#' @param ylim Limit of y axis
#' @param ylab Label of y axis
#' @param outma outma for setting par
#' @param margin margin for setting par
#' @param mgp mgp for setting par
#' @param legend.text Text for the legend
#' @param legend.color List of color for the legend
#' @param legend.xy x and y position of the legend
#' @param ... passed to graphics::boxplot function
boxplotTwoFactors <- function(data,
                              dv="vd",
                              iv1="vi1",
                              iv2="vi2",
                              colors=c("red","gray","red","gray"),
                              ylim=c(0,1),
                              ylab="",
                              outma=c(0.5,1,0.5,1),
                              margin=c(1,2,1,1),
                              mgp=c(1,0.2,0),
                              legend.text="",
                              legend.color="",
                              legend.xy="",
                              ...)
{
  par(oma=outma,mar=margin,mgp=mgp)
  graphics::boxplot(data[,dv]~data[,iv1]*data[,iv2],las=1,
          frame.plot=FALSE,axes=FALSE,outline=FALSE,
          col=colors,
          at=c(1,2,4,5),ylim=ylim,...)
  # axis(side = 1, at=0:2,pos=0, tck=-0.05,cex.axis=0.6,labels=c("","",""))
  par(mgp=mgp)
  graphics::axis(side = 2,las=1, pos=0,tck=-0.05,cex.axis=0.6,xpd=TRUE)
  graphics::title(ylab=ylab,mgp=mgp,cex=0.6)
  if(legend.text[1]!=""){
    par(xpd=T) # remove clipping so part of the legend can be outside the plot
    graphics::legend(legend.xy[1], legend.xy[2], legend=legend.text,col=legend.color, lty=1, lwd = 2, cex=0.6,bty = "n")
  }
}

#' Plot points in 2d
#'
#' Just a wrapper around plot and points functions.
#'
#' @param data data.frame with the data
#' @param v1 Name of the variable to plot on the x axis
#' @param v2 Name of the variable to plot on the y axis
#' @param axis.y.pos Position of the y axis
#' @param axis.x.pos Position of the x axis
#' @param axis.y.las Orientation of the letters for the label of the y axis
#' @param main.title Main title
#' @param mgp.x mgp for x axis
#' @param mgp.y mgp for y axis
#' @param xlab Label for the x axis
#' @param ylab Label for the y axis
#' @param plotxlim Limit of the x axis
#' @param plotylim Limit of the y axis
#' @param outma outma for setting par
#' @param margin margin for setting par
#' @param xaxis.at Where the tics are shown on the x axis
#' @param yaxis.at Where the tics are shown on the y axis
#' @param cex.point cex for the size of the points
#' @param add.text Text to add to the plot
#' @param add.text.pos Position of the text to add, format (x,y)
#' @param ... Passed to the graphics::plot function
plotPoints <- function(data,v1="v1",v2="v2",axis.y.pos=-.2,axis.x.pos=-.2,axis.y.las=2,
                        main.title="",mgp.x=c(0.5,0.1,0.1),mgp.y=c(0.9,0.2,0.1),xlab="",ylab="",
                        plotxlim=c(-.2,0.6),plotylim=c(-0.2,0.6),outma=c(0.5,0.5,0.5,0.5),margin=c(1.5,1.5,1,0.3),
                        xaxis.at=seq(-0.2,0.7,.2),yaxis.at=seq(-0.2,0.7,.2),cex.point=0.1,
                        add.text="",
                        add.text.pos=c(0,0.5),...)
{
  par(mar=margin, oma=outma,cex.lab=0.6,cex.axis=0.6)
  graphics::plot(x=plotxlim,y=plotylim,type='n', axes=FALSE, pch=20,lwd=1,xlab="",ylab="",...)
  points(data[,v1],data[,v2],pch=20,cex=cex.point)
  par(mgp=mgp.x)
  graphics::axis(side = 1, at=xaxis.at, pos=axis.x.pos,tck=-0.05,cex.axis=0.6)
  par(mgp=mgp.y)
  graphics::axis(side = 2, at=yaxis.at, las=axis.y.las, pos=axis.y.pos,tck=-0.05,cex.axis=0.6)
  graphics::title(xlab=xlab,mgp=mgp.x)
  graphics::title(ylab=ylab,mgp=mgp.y)
  if(main.title!=""){
    graphics::title(main=main.title,cex.main=0.4)
  }
  if(add.text!=""){
    graphics::text(labels=add.text,x=add.text.pos[1],y=add.text.pos[2],cex=0.6)
  }
}




#' Plot a single spike-time autocorrelation
#'
#' @param x Numeric vectors with the x values
#' @param y Numeric vectors with the y values
#' @param name Character vectors containing the name of the graph
#' @param axis.y.pos Position of the y axis
#' @param axis.x.pos Position of the x axis
#' @param axis.y.las Orientation of the letters for the label of the y axis
#' @param mgp.x mgp for x axis
#' @param mgp.y mgp for y axis
#' @param xlab Label for the x axis
#' @param ylab Label for the y axis
#' @param plotxlim Limit of the x axis
#' @param plotylim Limit of the y axis
#' @param outma outma for setting par
#' @param margin margin for setting par
#' @param xaxis.at Where the tics are shown on the x axis
#' @param yaxis.at Where the tics are shown on the y axis
#' @param add.text Text to add to the plot
#' @param add.text.pos Position of the text to add, format (x,y)
#' @param ... Passed to the lines function
spikeTimeAutocorrelationPlot <- function(x,y,name="",
                                         axis.y.pos=NA,axis.x.pos=0,
                                         axis.y.las=2,
                                         mgp.x=c(0.5,0.1,0.1), mgp.y=c(0.9,0.2,0.1),
                                         xlab="Time (ms)", ylab="Spikes",
                                         plotxlim=NA,plotylim=NA,
                                         outma=c(0.5,0.5,0.5,0.5),margin=c(1.5,1.5,1,0.3),
                                         xaxis.at=NA,yaxis.at=NA,
                                         add.text="",add.text.pos=c(0,0.5),...)
{
   par(mar=margin, oma=outma,cex.lab=0.6,cex.axis=0.6)
  if(is.na(plotxlim))
      plotxlim=c(min(x),max(x))
  if(is.na(plotylim))
    plotylim=c(0,max(y))
  if(is.na(axis.y.pos))
    axis.y.pos<-min(x)
  if(length(x)!=length(y))
    stop("length(x) != length(y)")
  graphics::plot(x=plotxlim,y=plotylim,type='n', axes=FALSE, pch=20,lwd=1,xlab="",ylab="")
  lines(x,y,...)
  par(mgp=mgp.x)
  if(is.na(xaxis.at)){
    graphics::axis(side = 1, pos=axis.x.pos, tck=-0.05,cex.axis=0.6)
  }else{
    graphics::axis(side = 1, pos=axis.x.pos, at=xaxis.at, tck=-0.05,cex.axis=0.6)
  }
  par(mgp=mgp.y)
  if(is.na(yaxis.at)){
    graphics::axis(side = 2, las=axis.y.las, pos=axis.y.pos,tck=-0.05,cex.axis=0.6)
  } else{
    graphics::axis(side = 2, at=yaxis.at, las=axis.y.las, pos=axis.y.pos,tck=-0.05,cex.axis=0.6)
  }
  graphics::title(xlab=xlab,mgp=mgp.x)
  graphics::title(ylab=ylab,mgp=mgp.y)
  if(name!=""){
    graphics::title(main=name,cex.main=0.5)
  }
  if(add.text!=""){
    graphics::text(labels=add.text,x=add.text.pos[1],y=add.text.pos[2],cex=0.6)
  }
}

#' Plot several spike-time autocorrelation plot on the same page
#'
#' @param autos A matrix containing autocorrelations
#' @param timePoints A numerical vector with the time point for each value of the autocorrelation
#' @param type Type of plot: 'l' for line or 'h' for barplot/histogram
#' @param names A character vector containing the name of each map in the array
#' @param ncol Number of columns of plots per page
#' @param nrow Number of rows of plots per page
spikeTimeAutocorrelationsPlot<-function(autos,timePoints,type,names,ncol=5,nrow=6){
  if (missing(type)) {
      type = 'l'
  }
  plot.per.page=ncol*nrow
  m<-matrix(c(rep(seq(0,1-(1/ncol),1/ncol),nrow),
              rep(seq(1/ncol,1,1/ncol),nrow),
              rep(seq(1-(1/nrow),0,0-1/nrow),each=ncol),
              rep(seq(1,1/nrow,0-1/nrow),each=ncol)),ncol=4)
  index=1
  nCells<-dim(autos)[2]
  for (i in 1:nCells){
    if(index==1)
    {
      split.screen(m)
    }
    screen(index)
    ## insert your plot function here
    spikeTimeAutocorrelationPlot(x=timePoints,y=autos[,i],type=type,name=names[i])
    if(index==plot.per.page)
    {
      close.screen( all.screens = TRUE )
      index=0
    }
    index=index+1
  }
  close.screen(all.screens = TRUE)
}

#' Plot function to display the recording trials of each recording session in a sessionList
#'
#' Easy way to visualize the environment used in each trial of a list of recording sessions
#'
#' @param sessionList List of RecSession objects
#' @param outma outma for setting par
#' @param margin margin for setting par
#' @param mgp.x mgp.x for setting par of xaxis
#' @param mgp.y mgp.y for setting par of yaxis
#' @param ylim ylim of the plot
recSessionListTrialPlot<- function(sessionList,
                                   outma=c(1,1,0.5,0.5),
                                   margin=c(1.5,1.5,1,0.3),
                                   mgp.x=c(0.5,0.2,0),
                                   mgp.y=c(0.8,0.2,0),
                                   ylim=NA)
{
  if(class(sessionList)!="list")
    stop("sessionList is not a list in ")
  if(class(sessionList[[1]])!="RecSession")
    stop("sessionList[[1]] is not a RecSession object")
  ## get time of each trial
  timeList<-lapply(sessionList,function(rs){rs@trialDurationSec/60})
  ## get environments
  envList<-lapply(sessionList,function(rs){rs@environment})
  ## get unique environments
  env<-unique(unlist(envList))
  ## cumulative time of trials
  cumSumTimeList<-lapply(timeList,function(tl){c(0,cumsum(tl))})
  xlim<-c(0,length(sessionList)+1)
  if(any(is.na(ylim)))
    ylim<-c(0,max(sapply(timeList,function(x){sum(x)})))
  par(mar=margin, oma=outma,cex.lab=0.6,cex.axis=0.6)
  graphics::plot(x=xlim,y=ylim,type='n', axes=FALSE, pch=20,lwd=1,xlab="",ylab="")
  ## make a rectangle for each trial in the experiment
  for(session in 1:length(envList))
    for(trial in 1:length(envList[[session]]))
      graphics::rect(xleft=session-0.4,xright = session+0.4,
                     ybottom = cumSumTimeList[[session]][trial],
                     ytop = cumSumTimeList[[session]][trial+1],
                     col=which(env==envList[[session]][trial]))
  ## y axis
  graphics::axis(side = 2,las=1, pos=0,tck=-0.05,cex.axis=0.6,xpd=TRUE)
  graphics::axis(side = 1,las=1, pos=0,tck=-0.05,cex.axis=0.6,xpd=TRUE)
  ## add a legend
  graphics::legend(x=xlim[2]-10, y=ylim[2],legend = env,fill=c(1:length(env)),cex=0.7,bg='lightblue')
  ## add title for x and y axis
  graphics::title(xlab="Sessions",mgp=mgp.x,cex=0.6)
  graphics::title(ylab="Time (min)",mgp=mgp.y,cex=0.6)
}



#' Plot a power spectrum
#'
#' @param x Numeric vectors with the x values
#' @param y Numeric vectors with the y values
#' @param name Character vectors containing the name of the graph
#' @param axis.y.pos Position of the y axis
#' @param axis.x.pos Position of the x axis
#' @param axis.y.las Orientation of the letters for the label of the y axis
#' @param mgp.x mgp for x axis
#' @param mgp.y mgp for y axis
#' @param xlab Label for the x axis
#' @param ylab Label for the y axis
#' @param plotxlim Limit of the x axis
#' @param plotylim Limit of the y axis
#' @param outma outma for setting par
#' @param margin margin for setting par
#' @param xaxis.at Where the tics are shown on the x axis
#' @param yaxis.at Where the tics are shown on the y axis
#' @param add.text Text to add to the plot
#' @param add.text.pos Position of the text to add, format (x,y)
#' @param ... Passed to the lines function
powerSpectrumPlot <- function(x,y,name="",
                              axis.y.pos=NA,axis.x.pos=0,
                              axis.y.las=2,
                              mgp.x=c(0.5,0.1,0.1), mgp.y=c(0.9,0.2,0.1),
                              xlab="Frequency (Hz)", ylab="Power",
                              plotxlim=NA,plotylim=NA,
                              outma=c(0.5,0.5,0.5,0.5),margin=c(1.5,1.5,1,0.3),
                              xaxis.at=NA,yaxis.at=NA,
                              add.text="",add.text.pos=c(0,0.5),...)
{
  par(mar=margin, oma=outma,cex.lab=0.6,cex.axis=0.6)
  if(any(is.na(plotxlim)))
    plotxlim=c(min(x),max(x))
  if(any(is.na(plotylim)))
    plotylim=c(0,max(y))
  if(any(is.na(axis.y.pos)))
    axis.y.pos<-min(x)
  if(length(x)!=length(y))
    stop("length(x) != length(y)")
  graphics::plot(x=plotxlim,y=plotylim,type='n', axes=FALSE, pch=20,lwd=1,xlab="",ylab="")
  lines(x,y,...)
  par(mgp=mgp.x)
  if(is.na(xaxis.at)){
    graphics::axis(side = 1, pos=axis.x.pos, tck=-0.05,cex.axis=0.6)
  }else{
    graphics::axis(side = 1, pos=axis.x.pos, at=xaxis.at, tck=-0.05,cex.axis=0.6)
  }
  par(mgp=mgp.y)
  if(is.na(yaxis.at)){
    graphics::axis(side = 2, las=axis.y.las, pos=axis.y.pos,tck=-0.05,cex.axis=0.6)
  } else{
    graphics::axis(side = 2, at=yaxis.at, las=axis.y.las, pos=axis.y.pos,tck=-0.05,cex.axis=0.6)
  }
  graphics::title(xlab=xlab,mgp=mgp.x)
  graphics::title(ylab=ylab,mgp=mgp.y)
  if(name!=""){
    graphics::title(main=name,cex.main=0.5)
  }
  if(add.text!=""){
    graphics::text(labels=add.text,x=add.text.pos[1],y=add.text.pos[2],cex=0.6)
  }
}