R/plotZSlice.R

In mknoll/imageanalysisBrain: Analysis of Brain Imaging Data

#' @title
#' Plot z slice of brainImage instance
#'  
#' @description
#' Plot given z slice of brainImage instance
#' 
#' @param data data.frame with x,y,z,val columns
#' @param z selected z slice to plot
#' @param index column with values to plot
#' @param ret return the image (T,F) as matrix
#' @param add add to existing plot
#' @param col color palette
#' @param main main
#' @param dimV dimension values: which are should be plotted?
#' min/max X,Y values
#' 
#' @return list of min/max values used for this plot
#' 
#' @import grDevices
#' @import EBImage
#' 
#' @export
#' 
#' @examples
#' data <- data.frame(x=rep(1:10, 5), 
#' y=c(rep(1,10),rep(2,10),rep(3,10),rep(4,10),rep(5, 10)), 
#' z=rep(1, 50), rnorm(50))
#' img <- new("brainImage", data, "test", 10)
#' plotZSlice(img, 1)
plotZSlice <- function(data, z, index=4, ret=FALSE, add=FALSE, 
                        col=grDevices::gray.colors(1024), main="", 
                        dimV=NULL)  {
    subD <- data@values[which(data@values$z == z), ]
    #subD <- data[which(data$z == z),]
    ## build image matrix
    if (is.null(dimV)) {
        minx <- min(subD$x, na.rm=TRUE)
        maxx <- max(subD$x, na.rm=TRUE)
        miny <- min(subD$y, na.rm=TRUE)
        maxy <- max(subD$y, na.rm=TRUE)
    } else {
        minx=dimV$minx
        miny=dimV$miny
        maxx=dimV$maxx
        maxy=dimV$maxy
    }
    
    imgM <- matrix(ncol=((maxx-minx)+1), nrow=((maxy-miny)+1), NA)
    i<-0
    
    for (y in miny:maxy) {
        i <- i+1
        if (!any(y %in% subD$y)) {
            next
        }
        vec <- rep(NA, maxx-minx+1)
        imgM[i,]<-vec
        row <- subD[which(subD$y == y),]
        vec[row$x-minx+1] <- row[,index]
        imgM[i,] <- vec
    }
    
    if (dim(imgM)[[2]] == 0) {
        return(NULL)
    }
    
    ##plot image
    EBImage::image(imgM, col=col, axes=FALSE, add=add, main=main)
    
    ##return dimensions used for this plot
    dim <- list(minx=minx, maxx=maxx, miny=miny, maxy=maxy)
    return(dim)
}