Nothing
#' Generic plotting of microbes over time
#' @param out output from microPopModel()
#' @param yLabel String for y axis label. Default is 'Concentration'
#' @param xLabel String for x axis label. Default is 'Time'
#' @param sumOverStrains Logical. Default=TRUE
#' @param legendPosition String. Position of legend in microbe plot, default is 'topleft'
#' @param cex.title Scaling for title text
#' @param cex.ax Scaling for axes text (labels and ticklabels)
#' @param cex.legend Scaling for legend text
#' @return Nothing just generates a plot
#' @importFrom graphics legend lines plot
#' @export
plotMicrobes = function(out,
sumOverStrains=TRUE,
yLabel='Concentration',
xLabel='Time',
legendPosition="topleft",
cex.title=1,
cex.ax=1,
cex.legend=1
){
soln=out$solution
numR=length(out$parms$resourceNames)
numStrains=out$parms$numStrains
microbeNames=out$parms$microbeNames
numMFG = length(microbeNames)
if (length(numStrains)==1){
numM = numStrains * numMFG
}else{
numM =sum(numStrains)
}
time = soln[, 1]
if (numM == 1) {
# one strain and one group (need to keep as a matrix)
X = as.matrix(soln[, 2:(numM + 1)])
colnames(X) = colnames(soln)[2]
} else {
X = soln[, 2:(numM + 1)]
}
if (any(numStrains > 1) & sumOverStrains) {
gmat = matrix(NA, nrow = length(time), ncol = numMFG)
for (g in 1:numMFG) {
gname=microbeNames[g]
ssum=rep(0,length(time))
for (strain in colnames(X)){
if (!is.na(pmatch(gname,strain))){
ssum = ssum + X[,strain]
}
}
gmat[, g] = ssum
}
Xmax = max(gmat, na.rm = TRUE)
} else {
Xmax = max(X, na.rm = TRUE)
}
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 = cex.ax, cex.axis = cex.ax, cex.main = cex.title,
type = "n")
for (g in 1:numMFG) {
gname=microbeNames[g]
if (any(numStrains > 1) & sumOverStrains) {
lines(time, gmat[, g], lwd = 2, col = cols[g])
} else {
for (strain in colnames(X)){
if (!is.na(pmatch(gname,strain))){
lines(time,X[,strain],lwd=2,col=cols[g])
}
}
}
}
legend(legendPosition, bg = "transparent", legend = microbeNames, col = cols, lty = 1,
lwd = 2,cex=cex.legend)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.