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library(ggplot2)
library(scales)
library(grid)
library(gridExtra)
library(reshape2)
# Filenames
args <- commandArgs(TRUE)
analysisdir <- args[1];
graphsdir <- args[2];
samplelist <- args[3];
outdir <- args[4];
format <- args[5];
types = c("2D", "Template", "Complement");
colours = c("#68B5B9", "#CF746D", "#91A851");
if (format=="png") {
textsize <- c(40)
pointsize <- c(5)
pointalpha <- c(0.5)
pointshape <- c(1)
pointwidth <- c(3)
xvjust <- c(1.2)
yvjust <- c(1.8)
} else {
textsize <- c(10)
pointsize <- c(2)
pointalpha <-c(0.4)
pointshape <- c(1)
pointwidth <- c(1)
xvjust <- c(0.2)
yvjust <- c(0.8)
}
data_samples = read.table(samplelist, header=TRUE);
for (t in 1:3) {
colourcode = colours[t];
# Gather data for box plots of length
df <- data.frame();
listOfDataFrames <- NULL;
count <- c(1);
for (i in 1:nrow(data_samples)) {
type = types[t];
sampledir <- data_samples[i, "SampleDir"];
filename_lengths <- paste(sampledir, "/", analysisdir, "/", "all_",type,"_lengths.txt", sep="");
data_lengths = read.table(filename_lengths, col.name=c("name", "length"));
#df$size <- data_lengths$length;
thisid <- data_samples[i, "SampleName"];
#paste(data_samples[i, "SampleName"], type, sep="_");
thisid
listOfDataFrames[[count]] <- data.frame(Sample=thisid, Length=data_lengths$length);
count <- count + 1;
}
# Read lengths
imagewidth <- 1 + (nrow(data_samples) * 0.5);
df <- do.call("rbind", listOfDataFrames);
output_file <- paste(graphsdir, "/", type, "_lengths.pdf", sep="");
message(output_file);
pdf(output_file, width=imagewidth, height = 4);
print(ggplot(df, aes(x=Sample, y=Length, fill=Sample)) + geom_boxplot() + theme(axis.text.x = element_text(angle = 45, hjust = 1)) + guides(fill=FALSE) + theme(text = element_text(size=textsize)) + ggtitle(types[t]));
garbage <- dev.off();
# Bar stacked plot of mapping
imagewidth <- 1 + (nrow(data_samples) * 0.5) + 1.5;
filename_maps <- paste(outdir, "/", type,"_map_summary.txt", sep="");
message(filename_maps)
#filename_maps <- c("~/temp/2D_map_summary.txt");
data_maps = read.table(filename_maps, header=TRUE);
df <- melt(data_maps, id.var="Sample")
output_file <- paste(graphsdir, "/", type, "_maps.pdf", sep="");
message(output_file);
pdf(output_file, width=imagewidth, height = 4);
print(ggplot(df, aes(x = Sample, y = value, fill = variable)) + geom_bar(stat = "identity") + theme(axis.text.x = element_text(angle = 45, hjust = 1)) + theme(text = element_text(size=textsize)) + ggtitle(types[t]) + ylab("%"));
garbage <- dev.off();
imagewidth <- 1 + (nrow(data_samples) * 0.5);
# Number of reads
filename_comparison <- paste(outdir, "/", type,"_comparison.txt", sep="");
data_comparison = read.table(filename_comparison, header=TRUE);
output_file <- paste(graphsdir, "/", type, "_number_of_reads.pdf", sep="");
message(output_file);
pdf(output_file, width=imagewidth, height = 4);
print(ggplot(data_comparison, aes(x=data_comparison$Name, y=data_comparison$NumReads)) + geom_bar(stat="identity", fill=colourcode) + ggtitle(type) + theme(text = element_text(size=textsize)) + xlab("Sample") + ylab("Number of reads") + theme(plot.margin = unit(c(0.02,0.02,0.04,0.02), "npc")) + theme(axis.title.y=element_text(vjust=0.2)) + theme(axis.title.x=element_text(vjust=-0.2)) + theme(plot.margin = unit(c(0.02,0.02,0.04,0.02), "npc")) + theme(axis.title.x=element_text(vjust=-xvjust)) + theme(axis.title.y=element_text(vjust=yvjust)) + theme(axis.text.x = element_text(angle = 45, hjust = 1)))
garbage <- dev.off();
# Total bases
data_comparison = read.table(filename_comparison, header=TRUE);
output_file <- paste(graphsdir, "/", type, "_total_bases.pdf", sep="");
message(output_file);
pdf(output_file, width=imagewidth, height = 4);
print(ggplot(data_comparison, aes(x=data_comparison$Name, y=data_comparison$TotalBases)) + geom_bar(stat="identity", fill=colourcode) + ggtitle(type) + theme(text = element_text(size=textsize)) + xlab("Sample") + ylab("Total bases") + theme(plot.margin = unit(c(0.02,0.02,0.04,0.02), "npc")) + theme(axis.title.y=element_text(vjust=0.2)) + theme(axis.title.x=element_text(vjust=-0.2)) + theme(plot.margin = unit(c(0.02,0.02,0.04,0.02), "npc")) + theme(axis.title.x=element_text(vjust=-xvjust)) + theme(axis.title.y=element_text(vjust=yvjust)) + theme(axis.text.x = element_text(angle = 45, hjust = 1)))
garbage <- dev.off();
}
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