R/quickPlot.R

In HelenKettle/microPop: Modelling Microbial Populations

#' Generic plotting showing results of microPop
#' @param out Output from microPopModel()
#' @param numR Scalar. Number of resources
#' @param numStrains Scalar. Number of strains per group
#' @param microbeNames Vector of strings which contains the names of the microbial groups in the system e.g. c('Bacteroides','Acetogens')
#' @param yLabel String for y axis label
#' @param xLabel String for x axis label
#' @param sumOverStrains Logical
#' @param saveFig Logical
#' @param figType String
#' @param figName String
#' @return Nothing just generates a plot
#' @importFrom grDevices dev.copy2eps dev.copy2pdf dev.new rainbow tiff dev.print png
#' @importFrom graphics legend lines par plot
#' @export
quickPlot = function(out, numR, numStrains, microbeNames, yLabel, xLabel, sumOverStrains, 
    saveFig = FALSE, figType = "eps", figName = "microPopFig") {
    
    wlen = 7
    hlen = 7  #width and height for png files
    
    numMFG = length(microbeNames)
    numM = numStrains * numMFG
    time = out[, 1]
    
    if (numM == 1) {
        # one strain and one group (need to keep as a matrix)
        X = as.matrix(out[, 2:(numM + 1)])
        colnames(X) = colnames(out)[2]
    } else {
        X = out[, 2:(numM + 1)]
    }
    
    R = out[, (numM + 2):(numM + numR + 1), drop = FALSE]
    
    if (numStrains > 1 & sumOverStrains) {
        gmat = matrix(NA, nrow = length(time), ncol = numMFG)
        for (g in 1:numMFG) {
            st = (g - 1) * numStrains + 1
            fin = g * numStrains
            gmat[, g] = rowSums(X[, st:fin])
        }
        Xmax = max(gmat, na.rm = TRUE)
    } else {
        Xmax = max(X, na.rm = TRUE)
    }
    
    if (figType == "png") {
        dev.new(bg = "white", horizontal = FALSE, onefile = FALSE, paper = "special", 
            width = wlen, height = hlen)
    } else {
        dev.new()
    }
    par(mar = c(5, 5, 5, 2))
    cols = rainbow(numMFG)  #different groups have different colours
    plot(range(time), c(min(0, min(X, na.rm = TRUE)), 1.1 * Xmax), xlab = xLabel, 
        main = "Microbes", ylab = yLabel, cex.lab = 1.5, cex.axis = 1.3, cex.main = 1.5, 
        type = "n")
    for (g in 1:numMFG) {
        if (numStrains > 1 & sumOverStrains) {
            lines(time, gmat[, g], lwd = 2, col = cols[g])
        } else {
            for (i in 1:numStrains) {
                j = (g - 1) * numStrains + i
                lines(time, X[, j], lwd = 2, col = cols[g])
            }
        }
    }
    legend("topleft", bg = "transparent", legend = microbeNames, col = cols, lty = 1, 
        lwd = 2)
    if (saveFig) {
        if (figType == "pdf") {
            dev.copy2pdf(file = paste(figName, "Microbes.pdf", sep = ""))
        }
        if (figType == "eps") {
            dev.copy2eps(file = paste(figName, "Microbes.eps", sep = ""))
        }
        if (figType == "png") {
            dev.print(png, filename = paste(figName, "Microbes.png", sep = ""), res = 100, 
                width = wlen, height = hlen, units = "in")
        }
        if (figType == "tiff") {
            dev.print(tiff, filename = paste(figName, "Microbes.tiff", sep = ""), 
                res = 100, width = wlen, height = hlen, units = "in")
        }
    }
    
    if (figType == "png") {
        wlen = 7
        hlen = 7
        dev.new(bg = "white", horizontal = FALSE, onefile = FALSE, paper = "special", 
            width = wlen, height = hlen)
    } else {
        dev.new()
    }
    par(mar = c(5, 5, 5, 2))
    cols = rainbow(numR)
    plot(range(time), c(min(0, min(R, na.rm = TRUE)), 1.1 * max(R, na.rm = TRUE)), 
        xlab = xLabel, main = "Resources", ylab = yLabel, cex.lab = 1.5, cex.axis = 1.3, 
        type = "n", cex.main = 1.5)
    for (i in 1:numR) {
        lines(time, R[, i], lwd = 2, col = cols[i])
    }
    legend("topleft", bg = "transparent", colnames(R), col = cols, lty = 1, lwd = 2)
    if (saveFig) {
        if (figType == "pdf") {
            dev.copy2pdf(file = paste(figName, "Resources.pdf", sep = ""))
        }
        if (figType == "eps") {
            dev.copy2eps(file = paste(figName, "Resources.eps", sep = ""))
        }
        if (figType == "png") {
            dev.print(png, filename = paste(figName, "Resources.png", sep = ""), 
                res = 100, width = wlen, height = hlen, units = "in")
        }
        if (figType == "tiff") {
            dev.print(tiff, filename = paste(figName, "Resources.tiff", sep = ""), 
                res = 100, width = wlen, height = hlen, units = "in")
        }
    }
    
}