mplight/shiny_light_transcriptomes_functions.r at main · Gregor-Mendel-Institute/mplight · GitHub

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require(magicaxis)

ssp_plot_lines <<- function(matn, metad, reg=1, gene,
						  plot_far_red=FALSE,
						  plot_pdf=FALSE,
						  plot_png=FALSE,
						  time_factors_d = c(1,4,5,3,6,2),
						  time_factors_nd = c(3,4,2,5,1),
						  plot_interactive=TRUE,
						  plot_filename = NULL,
						  basedir = "/groups/dolan/lab/members/Zohar/figures/",
						  myDate = substr(Sys.time(),1,10)) {
metad_levels = sort(as.numeric(names(table(metad$time))))
metad$time = factor(metad$time,levels = metad_levels)

e_d = matn[gene,grepl("^Dark_",colnames(matn))][time_factors_d]
e_w = matn[gene,grepl("^White_",colnames(matn))][time_factors_nd]
e_r = matn[gene,grepl("^Red_",colnames(matn))][time_factors_nd]
e_b = matn[gene,grepl("^Blue_",colnames(matn))][time_factors_nd]

if (plot_far_red) {
e_fr = matn[gene,grepl("^FarRed_",colnames(matn))][time_factors_nd] }


if (plot_far_red) {
y_range = c(0,max(c(e_d,e_w,e_r,e_b,e_fr),na.rm=TRUE))
} else {
y_range = c(0,max(c(e_d,e_w,e_r,e_b),na.rm=TRUE))
}


if (plot_pdf & !is.null(plot_filename)) {
pdf(plot_filename,
	width=800/100,height=300/100)
} else if (plot_png & !is.null(plot_filename)) {
png(plot_filename,
	width=800,height=300,
	res=100)} else if (plot_interactive) {

par(mar=c(5,5,1,1),mgp=c(3,0.8,0), bty="L")
plot(e_d, lwd=3,type="b",pch=19,cex=1.5,col="black",
	 cex.axis=1.5,cex.lab=1.5,
	 ylim = y_range,
	 xaxt="n",
	 yaxt="n",
	 ylab = gene,
	 xlab = "Time (minutes)"
	 )
magaxis(2,cex=1.5,las=2,cex.axis=1.5,tcl=(-0.5))
axis(1,at=1:length(metad_levels),labels=metad_levels,cex.axis=1.5)
lines(2:length(metad_levels),e_w,lwd=3,type="b",pch=19,cex=1.5,col="navajowhite2")
lines(2:length(metad_levels),e_r,lwd=3,type="b",pch=19,cex=1.5,col="red")
lines(2:length(metad_levels),e_b,lwd=3,type="b",pch=19,cex=1.5,col="blue")
	if (plot_far_red) {
lines(2:length(metad_levels),e_fr,lwd=3,type="b",pch=19,cex=1.5,col="red3")
	}
}

if ((plot_pdf | plot_png)) { dev.off() }
}