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plot_energy_bands.R
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plot_energy_bands.R
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#!/usr/bin/env Rscript
#
library("optparse")
library("ggplot2")
library("ggpubr")
library("scico")
cbPalette <- c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
bwPalette <- c("#eeeeee", "#aaaaaa", "#777777", "#444444", "#111111")
cbPalette <- c("#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7", "#999999")
cbPalette <- c("#999999", "#E69F00", "#009E73", "#D55E00", "#CC79A7")
cbPalette <- scico(4, palette = 'roma')
data_order = c("DrTrafo","Kinfold", "MFE","sampling")
data_labels = c("DrTransformer", "Kinfold", "RNAfold", "RNAsubopt")
strand_order = c("SRPn", "SRPt", "SRPr", "SRPf")
strand_labels = c("SRPn (native)", "SRPt (U21C)", "SRPr (U21C/C22U/G93A)", "SRPf (U35C/U37C)")
circle <- 1
circle_filled <- 21
square <- 0
square_filled <- 22
triangle_up <- 2
triangle_up_filled <- 24
diamond <- 5
diamond_filled <- 23
region_shapes_fill <- c(circle_filled, square_filled, triangle_up_filled, diamond_filled)
option_list = list(
make_option(c("-i", "--inputfile"), type="character", default=NULL,
help="dataset file name", metavar="character"),
make_option(c("-o", "--out"), type="character", default="plot.pdf",
help="output file name [default= %default]", metavar="character"),
make_option(c("-t", "--title"), type="character", default=NULL,
help="Plot title", metavar="character"),
make_option(c("-m","--minmax"), type="logical", action="store_true", default=FALSE,
help="Plot minimum- and maximum bands instead of 25 and 75 quantile borders"),
make_option(c("-s", "--start"), type="integer", default=-1,
help="Start value for y axis"),
make_option(c("-e", "--end"), type="integer", default=0,
help="End of transcription, i.e. maximum transcript length"),
make_option(c("--offset"), type="integer", default=0,
help="Offset of transcription time points"),
make_option(c("--noguide"), type="logical", action="store_true", default=FALSE,
help="Disable the guide, a.k.a. legend."),
make_option(c("-d","--dots"), type="logical", action="store_true", default=FALSE,
help="Add dots for each data point")
)
opt_parser = OptionParser(option_list=option_list);
opt = parse_args(opt_parser);
if (is.null(opt$inputfile)){
print_help(opt_parser)
stop("Specify at lease the input file", call.=FALSE)
}
dat <- read.table(opt$inputfile, head=T, sep=",")
if (opt$end == 0) {
end = max(dat$length)
} else {
end = opt$end
}
if (opt$start == -1) {
start = min(dat$length)
} else {
start = opt$start
}
x_axis_breaks = seq(start%/%10 * 10, end, 10)
print(start%/%10)
x_label = "Transcript Length [nt]"
if (opt$offset > 0) {
# adjust x-axis labels
x_axis_labels <- c()
for (i in x_axis_breaks) {
x_axis_labels <- c(x_axis_labels, sprintf('%d (%d)', i + opt$offset, i))
}
x_label = "Transcript Length (w/o footprint) [nt]"
} else {
x_axis_labels = x_axis_breaks
}
p <- ggplot(dat, aes(length,
fill=factor(method, levels = data_order, labels = data_labels),
color=factor(method, levels = data_order, labels = data_labels)
))
p <- p + geom_ribbon(aes(ymin=Q25, ymax=Q75),
alpha=0.4,
# colour = NA,
size = 0.1)
p <- p + geom_line(aes(length, Qmedian), size=2)
if (opt$dots) {
p <- p + geom_point(aes(length, Qmedian, shape = factor(method)),
size=2,
fill = "white",
data=subset(dat, length %% 5 == 0))
}
p <- p + facet_grid(~factor(name, levels=strand_order, labels = strand_labels))
p <- p + scale_x_continuous(expand = c(0, 0),
limit = c(start, end),
breaks = x_axis_breaks,
labels = x_axis_labels)
p <- p + scale_y_continuous(limit=c(-60, 15), breaks=seq(-60, 0, 10), expand = c(0,0))
p <- p + scale_fill_manual( values = cbPalette)
p <- p + scale_colour_manual( values = cbPalette)
#p <- p + scale_fill_scico_d( palette = "batlow")
#p <- p + scale_colour_scico_d( palette = "batlow")
#p <- p + scale_fill_brewer(palette = 'Paired')
#p <- p + scale_colour_brewer(palette = 'Paired')
p <- p + scale_shape_manual( breaks = data_order,
labels = data_labels,
values = region_shapes_fill )
p <- p + xlab(x_label)
p <- p + ylab(expression(paste("Free Energy [", kcal, ~mol^{-1}, "]")))
if (!is.null(opt$title)){
p <- p + ggtitle(opt$title)
}
p <- p + theme_bw()
p <- p + theme(plot.title = element_text(hjust = 0.5, size = 24),
plot.background = element_blank(),
# panel.grid.minor = element_blank(),
axis.line = element_blank(),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
panel.background = element_blank(),
strip.background = element_blank())
p <- p + theme(#axis.title.x = element_text(family="Helvetica", size = 16, colour="#000000"),
axis.title.x = element_blank(),
axis.text.x = element_text(family="Helvetica", size = 14, colour="#666666", angle = 90.),
axis.title.y = element_text(family="Helvetica", size = 16, colour="#000000"),
axis.text.y = element_text(family="Helvetica", size = 14, colour="#666666"),
strip.text.x = element_text(family="Helvetica", size = 20, colour="#111111")
)
if (opt$noguide) {
p <- p + theme(legend.position = "none")
} else {
p <- p + guides(
color = guide_legend(title = "Method"),
fill = guide_legend(title = "Method"),
shape = guide_legend(title = "Method")
)
p <- p + theme(legend.position = "bottom",
legend.title = element_blank(),
legend.text = element_text(size = 18),
legend.background = element_blank(),
legend.key.height = unit(2,"line"),
legend.key.width = unit(2,"line"))
}
p2 <- ggplot(dat, aes(length,
fill=factor(method, levels = data_order, labels = data_labels),
color=factor(method, levels = data_order, labels = data_labels)
))
p2 <- p2 + geom_ribbon(aes(ymin=Qmin, ymax=Qmax),
alpha=0.4,
# colour = NA,
size = 0.1,
linetype = 2)
p2 <- p2 + geom_line(aes(length, Qmean), size=2)
if (opt$dots) {
p2 <- p2 + geom_point(aes(length, Qmean, shape = factor(method)),
size=2,
fill = "white",
data=subset(dat, length %% 5 == 0))
}
p2 <- p2 + facet_grid(~factor(name, levels=strand_order, labels = strand_labels))
p2 <- p2 + scale_x_continuous(expand = c(0, 0),
limit = c(start, end),
breaks = x_axis_breaks,
labels = x_axis_labels)
p2 <- p2 + scale_y_continuous(limit=c(-60, 15), breaks=seq(-60, 0, 10), expand = c(0,0))
p2 <- p2 + scale_fill_manual( values = cbPalette)
p2 <- p2 + scale_colour_manual( values = cbPalette)
#p2 <- p2 + scale_fill_brewer(palette = 'Paired')
#p2 <- p2 + scale_colour_brewer(palette = 'Paired')
p2 <- p2 + scale_shape_manual( breaks = data_order,
labels = data_labels,
values = region_shapes_fill )
p2 <- p2 + xlab(x_label)
p2 <- p2 + ylab(expression(paste("Free Energy [", kcal, ~mol^{-1}, "]")))
if (!is.null(opt$title)){
p2 <- p2 + ggtitle(opt$title)
}
p2 <- p2 + theme_bw()
p2 <- p2 + theme(plot.title = element_text(hjust = 0.5, size = 20),
plot.background = element_blank(),
# panel.grid.minor = element_blank(),
axis.line = element_blank(),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
panel.background = element_blank(),
strip.background = element_blank(),
strip.text.x = element_blank())
p2 <- p2 + theme(axis.title.x = element_text(family="Helvetica", size = 16, colour="#000000"),
axis.text.x = element_text(family="Helvetica", size = 14, colour="#666666", angle = 90.,vjust=0.5),
axis.title.y = element_text(family="Helvetica", size = 16, colour="#000000"),
axis.text.y = element_text(family="Helvetica", size = 14, colour="#666666")
)
p2 <- p2 + theme(legend.position = "none")
ppp <- ggarrange(
p, p2,
labels = c("A", "B"),
font.label=list(color="black",size=32),
ncol = 1,
common.legend = TRUE, legend = "bottom"
)
ggsave(plot = ppp, file=opt$out, width=15, height=10)