kelshmo / analysis Goto Github PK

# How to plot a voom object if save.plot=TRUE

# Set plot generic to voom result EList
#' @export
setMethod("plot", signature(x="EList", y="missing"),
  function(x,  y, ...){

  	if( is.null(x$voom.xy) || is.null(x$voom.line)){
  		stop("x does not contain the trend information.\nvoom() must be run with save.plot=TRUE")
  	}

  	# points
	df = data.frame(x = x$voom.xy$x,
					y = x$voom.xy$y)

	# trend line
	df.line = data.frame(x = x$voom.line$x,
						y = x$voom.line$y)

	ggplot(df, aes(x,y)) + geom_point(size=.1) + theme_bw(15) + theme(aspect.ratio=1, plot.title = element_text(hjust = 0.5)) + geom_line(data=df.line, aes(x,y), color="red") + xlab(bquote(log[2](count + 0.5))) + ylab(expression( sqrt("standard deviation"))) + ggtitle("Voom: Mean-variance trend") + ylim(0, max(df$y))
  }
)