R/plotLocalizations_Density.R

In sheng-liu/smt-beta-0.3.9.1: Statistical analysis of single molecule trajectories

#### plotLocalizations_Density.R Wu Lab, Johns Hopkins University Author:
#### Xiaona Tang Date: Dec 20, 2017

## plotLocalizations_Density-methods
##' @name plotLocalizations_Density
##' @aliases plotLocalizations_Density
##' @title plotLocalizations_Density
##' @rdname plotLocalizations_Density-methods
##' @docType methods
##' @description Plot localization map of molecules from a list of files in a 
##' folder with color coded 
##' by local density of each molecule. 
##' 
##' @usage
##'
##' plotLocalizations_Density(trackll=trackll,scale=256,r=125,file.No=0,
##' point.scale=0.15)
##'
##' @param trackll trajectory list generated by createTrackll() and 
##' processing. if NULL, user will be prompted to enter the trackll name.
##' @param scale The pixel scale of image data.
##' @param r Radius within each molecule to calculate density in nanometer 
##' (nm).
##' @param file.No Select file(s) in the folder to plot. Default 0 for 
##' plotting all files in the folder.
##' @param point.scale Size of the dots representing the molecules.
##' @return
##' \itemize{
##' \item{PDF:} One PDF file with one plot on each page.
##' }
##' @details Plot localization map of molecules from a list of files in a 
##' folder with color coded 
##'         by local density of each molecule. The localization of molecule is 
##'         considered as the first position of its track. 
##'         
##'         Upon running of the function, users will be prompted to input the 
##'         name of the track list (trackll).
##'         Input un-merged trackll and the plotting will start.
##'         The local density of each molecule is calculated by counting the 
##'         number of molecules within a given radius
##'         around the position of the molecule. The higher the number, the 
##'         higher the local density.

##'
##' @examples
##'
##' # Generate trackll, and process, 
##' # e.g. mask region of interest, tracks from multiple files should not be 
##' # merged.
##' folder=system.file('extdata','HSF',package='sojourner')
##' trackll=createTrackll(folder=folder, input=3)
##' trackll=maskTracks(folder,trackll)
##' 
##' # Plot localization map,
##' plotLocalizations_Density(trackll=trackll,scale=128,
##'                           r=125,file.No=0,point.scale=0.3)
##' # Plot only file No. 2 and increase the point size,
##' plotLocalizations_Density(trackll=trackll,scale=128,
##'                           r=125,file.No=2,point.scale=1)
##' 
##' @importFrom sampSurf spCircle
##' @export plotLocalizations_Density

############################################################################### 


## Function for plotting molecule localizations with color coded by
## local molecule density.

.plotLocalizations.Density <- function(trackll = trackll, scale = 256, 
    r = 125, file.No = 0, point.scale = 0.15) {
    
    
    ## Import trackll (un-merged) information
    if (length(file.No) > 1 & min(file.No) == 0) {
        stop("Wrong file.No input. Ceased.", call. = FALSE, domain = NULL)
    }
    
    if (is.null(trackll)) {
        trackll.label <- readline(cat(
            "Enter the un-merged trackll you want to plot:    "))
        trackll <- get(paste(trackll.label))
    }
    
    if (length(file.No) >= 1 & file.No[1] > 0) {
        trackll <- trackll[file.No]
    }
    
    ## Set plot area as black background and white frontground.
    oldpar <- par
    par(mar = c(3, 4, 4, 3), xpd = FALSE)
    
    par(mfrow = c(1, 1), bg = "black", fg = "white")
    cat("Plotting...A PDF file will be output in the working directory.\n")
    
    ## Get trackl info and plot localization map for each file in the
    ## trackll.
    for (i in c(seq_along(trackll))) {
        plot.new()
        plot.window(xlim = c(0, scale * 0.107), ylim = c(0, scale * 0.107), 
            xaxs = "i", yaxs = "i")
        
        axis(1, cex.axis = 1, col.axis = "white")
        axis(2, cex.axis = 1, col.axis = "white")
        mtext(gsub(".mat", "", names(trackll[i])), side = 3, line = 0.5, 
            cex = 2, col.main = "white")
        mtext(expression(paste("X (", mu, "m)")), side = 1, line = 2, 
            cex.lab = 1, col = "white")
        mtext(expression(paste("Y (", mu, "m)")), side = 2, line = 2, 
            cex.lab = 1, col = "white")
        box()
        
        ## Get the localization of each track (molecule) as the first position
        ## of the track.
        localizations <- data.frame(matrix(ncol = 3, nrow = 0))
        for (j in c(seq_along(trackll[[i]]))) {
            localizations <- rbind(localizations, 
                setNames(data.frame(paste0(names(trackll[[i]][j])), 
                    trackll[[i]][[j]]$x[[1]] * 0.107, 
                    trackll[[i]][[j]]$y[[1]] * 0.107), 
                    c("Trajectory", "x", "y")))
        }
        ## Calculate local molecule density by counting the molecule number
        ## within a given radius.
        sp::coordinates(localizations) <- c("x", "y")
        for (k in c(seq_along(localizations$x))) {
            ## Generate a named vector 'cp' to make this loop work in both Mac 
            ## and PC version of R.
            cp = c(localizations[k, ]$x, localizations[k, ]$y)
            names(cp) = c("x", "y")
            sp.n = sampSurf::spCircle(r/1000, centerPoint = cp, spID = "tree.1")
            count.n <- sp::over(localizations, sp.n$spCircle)
            localizations$density[k] = sum(count.n, na.rm = TRUE)
        }
        
        ## Generate color gradient/ramp based on the highest molecule density in
        ## each file.  cl=grDevices::heat.colors(max(localizations$density))
        ## cl=colorspace::diverge_hsv(max(localizations$density))
        ## cl=colorspace::diverge_hcl(max(localizations$density))
        cl <- colorRampPalette(
            c("blue4", "white", "red"))(n = max(localizations$density))
        
        ## plot the molecules as dots color coded by it's local density.
        for (i in c(seq_along(localizations$x))) {
            points(localizations[i, ]$x, localizations[i, ]$y, pch = 16, 
                col = cl[localizations[i, ]$density], cex = point.scale)
        }
        ## Add color gradient legend to the right edge of each plot.
        .legend.col(col = cl, lev = localizations$density)
        ## Add radius and molecule number (n) as text legend to the topright
        ## corner of each plot.
        legend("topright", paste(rep(c("r = ", "n = ")), 
            rep(c(r, nrow(localizations))), rep(c(" nm", ""))), 
            col = "white", bty = "n")
        
    }
    
    ## Reset plotting area parameters.
    par(oldpar)
    par(mfrow = c(1, 1), bg = "white", fg = "black")
}




## Function for outputting the plots into one multipage PDF file in the
## working directory.

plotLocalizations_Density <- function(trackll = trackll, scale = 256, r = 125, 
    file.No = 0, point.scale = 0.15) {
    ## Output the plots into one PDF file in the working directory.
    pdf(paste("plotLocalization_Density_Heatmap--", format(Sys.time(), 
        "%Y%m%d_%H%M%S"), ".pdf", sep = ""), width = 11.7, height = 11.7)
    
    .plotLocalizations.Density(trackll = trackll, scale = scale, r = r, 
        file.No = file.No, point.scale = point.scale)
    
    dev.off()
}