R/pcaDotplot.R

In jasenfinch/OrbiFIEmisc: Miscellaneous functions for the analysis of FIE-HRMS data.

#' PCA variance dotplot using ggplot2
#' @export

pcaDotplot <- function(pca.vars,Path,DF){
	.e = environment()
	pca.vars <- melt(t(pca.vars))
  bitmap(paste(Path,DF,paste(DF,"PCA_&_LDA",sep="_"),paste(DF,"PCA_Variance.bmp" ,sep="_"),sep="/"))
	pca.p.1 <- ggplot(pca.vars,aes(x=Var2,y=value,colour=Var1),environment=.e) +
						 	geom_point(size=3,aes(shape=Var1)) +
						  coord_flip() +
							ylab("Percentage") +
							theme(plot.title = element_text(lineheight=.8, face="bold"),legend.title=element_blank() )  +
							scale_shape_manual(values=c(1:length(unique(pca.vars$Var1)))) +
							xlab("") +
							ggtitle(paste(DF,": PCA proportion of variance"))						
	print(pca.p.1)
	graphics.off()
}