R/plot.slidWin.R

In boopsboops/spider: Species Identity and Evolution in R

#' Plot a 'slidWin' object
#' 
#' Graphical representation of the summary statistics derived from
#' \code{\link{slideAnalyses}} and \code{\link{slideBoxplots}}
#' 
#' When boxplots of methods \code{nonCon} and \code{interAll}, the y-axis
#' limits are constrained to the midpoint of the range covered by the boxplots,
#' so that the intra-specific variation can be seen.
#' 
#' @param x An object of class `slidWin'.
#' @param outliers Logical. When the results of \code{\link{slideBoxplots}} are
#' being called, should the outliers be plotted? Default of FALSE.
#' @param ...  Other arguments to be passed to \code{plot}.
#' @return Plots graphs depending on the options given to
#' \code{\link{slideAnalyses}} or \code{\link{slideBoxplots}}.
#' @author Samuel Brown <s_d_j_brown@@hotmail.com>
#' @seealso \code{\link{slideAnalyses}}, \code{\link{slideBoxplots}}.
#' @keywords Sliding window
#' @examples
#' 
#' data(dolomedes)
#' doloSpp <- substr(dimnames(dolomedes)[[1]], 1, 5)
#' 
#' doloSlide <- slideAnalyses(dolomedes,  doloSpp, 200, interval=10, treeMeasures=TRUE)
#' 
#' graphics::plot(doloSlide)
#' 
#' doloBox <- slideBoxplots(dolomedes,  doloSpp, 200, interval=10, method="overall")
#' 
#' graphics::plot(doloBox)
#' 
#' 
#' data(anoteropsis)
#' anoSpp <- sapply(strsplit(dimnames(anoteropsis)[[1]], split="_"), 
#'     function(x) paste(x[1], x[2], sep="_"))
#' 
#' anoBox <- slideBoxplots(anoteropsis,  anoSpp, 200, interval=10, method="interAll")
#' 
#' graphics::plot(anoBox)
#' graphics::plot(anoBox, outliers=TRUE)
#' 
#' 
#' @importFrom graphics plot
#' @importFrom graphics abline
#' @importFrom graphics layout
#' @importFrom graphics axis
#' @importFrom graphics bxp
#' @importFrom stats median
#' @export
plot.slidWin <- 
function(x, outliers = FALSE, ...){
	slidWin <- x
	distM <- function(){
		plot(slidWin$pos_out, slidWin$dist_mean_out, xlab = "Window position", ylab = "Distance", main="Mean K2P distance of each window")
		ylimzero <- range(slidWin$zero_out, slidWin$dat_zero_out, na.rm=TRUE)
		plot(slidWin$pos_out, slidWin$zero_out, ylim = ylimzero, xlab = "Window position", ylab = "Proportion", main="Proportion of zero cells in K2P distance matrix")
			abline(h=slidWin$dat_zero_out)
		#thres_main <- paste("Number of cells above ", slidWin$thresA, " (black) and below ", slidWin$thresB, " (blue)", sep="")
		#ylimthres <- range(slidWin$thres_above_out, slidWin$thres_below_out, na.rm=TRUE)
		#plot(slidWin$pos_out, slidWin$thres_above_out, ylim = ylimthres, xlab = "Position", ylab = "Number of cells", main = thres_main)
			#points(slidWin$pos_out, slidWin$thres_below_out, col = "blue")
		plot(slidWin$pos_out, slidWin$nd_out, xlab = "Window position", ylab = "Number", main = "Sum of diagnostic nucleotides", type="l")
		plot(slidWin$pos_out, slidWin$noncon_out, ylim=c(0, max(slidWin$noncon_out)), xlab = "Window position", ylab = "Proportion", main = "Proportion of zero non-conspecific K2P distances")
	}

	distT <- function(){
		ylimcomp <- range(slidWin$comp_out, slidWin$comp_depth_out, na.rm=TRUE)
		plot(slidWin$pos_tr_out, slidWin$comp_out, ylim = ylimcomp, xlab = "Window position", ylab = "Proportion", main="Congruence of NJ trees")
		#	points(slidWin$pos_tr_out, slidWin$comp_depth_out, col="blue")
		plot(slidWin$pos_tr_out, slidWin$win_mono_out, xlab = "Window position", ylab = "Proportion", main = "Proportion of species that are monophyletic")
	}

	if(slidWin$boxplot_out){
		layout(1)
		if(slidWin$method == "overall"){
			plot(1, type = "n", xlim = c(1,length(slidWin$bp_out)), ylim = slidWin$bp_range_out, xaxt = "n", main="Boxplot of distance matrix for each window", xlab="Window position", ylab="Distance")
			axis(1, at = 1:length(slidWin$bp_out), labels = as.character(slidWin$pos_out))
			for(i in 1:length(slidWin$bp_out)) bxp(slidWin$bp_out[[i]], at=i, add=TRUE, axes=FALSE, whisklty=1, whiskcol="red", staplelty=0, outpch=NA)
		}#x11()
		if(slidWin$method %in% c("interAll", "nonCon")){
			labs <- c("interAll", "nonCon")
			desc <- c("all inter-specific", "closest non-conspecific")
			plotTitle <- paste("Boxplots of", desc[which(slidWin$method==labs)], "distances (orange whiskers) and \nintra-specific distances (blue whiskers) in each window", sep=" ")
			plot(1, type = "n", xlim = c(1,length(slidWin$bp_InterSpp_out)), ylim = c(0, median(slidWin$bp_range_out)), xaxt = "n", main=plotTitle, xlab="Window position", ylab="Distance")
			axis(1, at = 1:length(slidWin$bp_InterSpp_out), labels = as.character(slidWin$pos_out))
			if(outliers){
				for(i in 1:length(slidWin$bp_InterSpp_out)) bxp(slidWin$bp_InterSpp_out[[i]], at=i, add=TRUE, axes=FALSE, whisklty=1, whiskcol="orange", staplelty=0, outpch=20, outcol="orange")
				for(i in 1:length(slidWin$bp_IntraSpp_out)) bxp(slidWin$bp_IntraSpp_out[[i]], at=i, add=TRUE, axes=FALSE, whisklty=1, whiskcol="blue", staplelty=0, outpch=20, outcol="blue", outcex=0.75)
			}
			else{
				for(i in 1:length(slidWin$bp_InterSpp_out)) bxp(slidWin$bp_InterSpp_out[[i]], at=i, add=TRUE, axes=FALSE, whisklty=1, whiskcol="orange", staplelty=0, outpch=NA)
				for(i in 1:length(slidWin$bp_IntraSpp_out)) bxp(slidWin$bp_IntraSpp_out[[i]], at=i, add=TRUE, axes=FALSE, whisklty=1, whiskcol="blue", staplelty=0, outpch=NA)
			}
		}
	}

	if(slidWin$distMeasures && slidWin$treeMeasures){
		layout(matrix(1:6, ncol=2))
		distM()
		distT()
	} else {
			if(slidWin$distMeasures) {
				layout(1:4)
				distM() }
			if(slidWin$treeMeasures){
				layout(1:2)
				distT()}				
		}
layout(1)
}