R/plot.iris.R

In KO-BMI/umap-viz: What the Package Does (One Line, Title Case)

#' Umap Plot
#'
#' @export plot.iris

plot.iris<-function(x, labels,
                    main="A UMAP visualization of the Iris dataset",
                    colors=c("#ff7f00", "#e377c2", "#17becf"),
                    pad=0.1, cex=0.65, pch=19, add=FALSE, legend.suffix="",
                    cex.main=1, cex.legend=1) {
           
             layout = x
             if (is(x, "umap")) {
               layout = x$layout
             } 
             
             xylim = range(layout)
             xylim = xylim + ((xylim[2]-xylim[1])*pad)*c(-0.5, 0.5)
             if (!add) {
               par(mar=c(0.2,0.7,1.2,0.7), ps=10)
               plot(xylim, xylim, type="n", axes=F, frame=F)
               rect(xylim[1], xylim[1], xylim[2], xylim[2], border="#aaaaaa", lwd=0.25)  
             }
             points(layout[,1], layout[,2], col=colors[as.integer(labels)],
                    cex=cex, pch=pch)
             mtext(side=3, main, cex=cex.main)
           
             labels.u = unique(labels)
             legend.pos = "topright"
             legend.text = as.character(labels.u)
             if (add) {
               legend.pos = "bottomright"
               legend.text = paste(as.character(labels.u), legend.suffix)
             }
             legend(legend.pos, legend=legend.text,
                    col=colors[as.integer(labels.u)],
                    bty="n", pch=pch, cex=cex.legend)
           }