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Merge pull request #128 from drpatelh/dev
Add plots for consensus QC
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| #!/usr/bin/env Rscript | ||
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| ################################################ | ||
| ################################################ | ||
| ## LOAD LIBRARIES ## | ||
| ################################################ | ||
| ################################################ | ||
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| library(optparse) | ||
| library(ggplot2) | ||
| library(scales) | ||
| library(reshape2) | ||
| library(Biostrings) | ||
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| ################################################ | ||
| ################################################ | ||
| ## VALIDATE COMMAND-LINE PARAMETERS ## | ||
| ################################################ | ||
| ################################################ | ||
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| option_list <- list(make_option(c("-i", "--fasta_files"), type="character", default=NULL, help="Comma-separated list of fasta files", metavar="fasta_files"), | ||
| make_option(c("-s", "--prefixes"), type="character", default=NULL, help="Comma-separated list of prefixes associated with fasta files to add to plots. Must be unique and in same order as fasta file input.", metavar="prefixes"), | ||
| make_option(c("-o", "--output_dir"), type="character", default='./', help="Output directory", metavar="path")) | ||
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| opt_parser <- OptionParser(option_list=option_list) | ||
| opt <- parse_args(opt_parser) | ||
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| ## Check input files | ||
| INPUT_FILES <- unique(unlist(strsplit(opt$fasta_files,","))) | ||
| if (length(INPUT_FILES) == 0) { | ||
| print_help(opt_parser) | ||
| stop("At least one input file must be supplied", call.=FALSE) | ||
| } | ||
| if (!all(file.exists(INPUT_FILES))) { | ||
| stop(paste("The following input files don't exist:",paste(INPUT_FILES[!file.exists(INPUT_FILES)], sep='', collapse=' '), sep=' '), call.=FALSE) | ||
| } | ||
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| ## Check prefixes for input files | ||
| PREFIXES <- basename(INPUT_FILES) | ||
| if (!is.null(opt$prefixes)){ | ||
| PREFIXES <- unique(unlist(strsplit(opt$prefixes,","))) | ||
| if (length(INPUT_FILES) != length(PREFIXES)) { | ||
| print_help(opt_parser) | ||
| stop("Please provide a unique prefix for each fasta file.", call.=FALSE) | ||
| } | ||
| } | ||
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| ## Check the output directory has a trailing slash, if not add one | ||
| OUTDIR <- opt$output_dir | ||
| if (tail(strsplit(OUTDIR,"")[[1]],1)!="/") { | ||
| OUTDIR <- paste(OUTDIR,"/",sep='') | ||
| } | ||
| ## Create the directory if it doesn't already exist. | ||
| if (!file.exists(OUTDIR)) { | ||
| dir.create(OUTDIR, recursive=TRUE) | ||
| } | ||
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| ################################################ | ||
| ################################################ | ||
| ## READ IN DATA ## | ||
| ################################################ | ||
| ################################################ | ||
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| dat <- NULL | ||
| for (input_file in INPUT_FILES) { | ||
| dat <- c(dat,readDNAStringSet(input_file)[1]) | ||
| } | ||
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| ################################################ | ||
| ################################################ | ||
| ## PLOTS ## | ||
| ################################################ | ||
| ################################################ | ||
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| bases_std <- c("A","C","T","G") | ||
| base_cols <- c("A" = "#009E73", | ||
| "C" = "#0072B2", | ||
| "T" = "#D55E00", | ||
| "G" = "#000000", | ||
| "N" = "#E69F00", | ||
| "X" = "#999999") | ||
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| for (idx in 1:length(dat)) { | ||
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| ## Table of base counts | ||
| base_seq <- strsplit(toString(dat[[idx]]), "")[[1]] | ||
| base_tab <- data.frame(table(base_seq), stringsAsFactors=FALSE) | ||
| colnames(base_tab) <- c("base","freq") | ||
| rownames(base_tab) <- base_tab$base | ||
| for (base in 1:length(bases_std)) { | ||
| if (!any(base_tab$base %in% bases_std[base])) { | ||
| base_tab <- rbind(base_tab,c(bases_std[base],0)) | ||
| } | ||
| } | ||
| base_tab$perc <- 100 *base_tab$freq / sum(base_tab$freq) | ||
| base_tab <- base_tab[order(base_tab$base, decreasing=FALSE),] | ||
| base_tab <- rbind(base_tab[c(bases_std, "N"),], base_tab[!rownames(base_tab) %in% c(bases_std, "N"),]) | ||
| base_tab$base <- factor(base_tab$base, levels=rownames(base_tab)) | ||
| outfile <- paste(OUTDIR, PREFIXES[idx], ".base_counts.tsv", sep='') | ||
| write.table(base_tab, file=outfile, col.names=TRUE, row.names=FALSE, sep="\t", quote=FALSE) | ||
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| ## Barplot of base frequencies | ||
| barplot <- ggplot(base_tab, aes(x=base,y=perc)) + | ||
| geom_bar(stat="identity") + | ||
| theme_classic() + | ||
| scale_y_continuous(limits=c(0,100),breaks=c(0,25,50,75,100)) + | ||
| ylab("% Observed") + | ||
| xlab("Base") + | ||
| ggtitle(PREFIXES[idx]) | ||
| outfile <- paste(OUTDIR, PREFIXES[idx], ".base_counts.pdf", sep='') | ||
| ggsave(file=outfile, barplot, width=12, height=10, units="cm") | ||
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| ## Create a data frame of base coverage | ||
| bases <- unique(c(bases_std,"N",unique(base_seq))) | ||
| base_dat <- data.frame(sample=names(dat[[idx]])[1], position=1:length(base_seq), stringsAsFactors=FALSE) | ||
| for (base in 1:length(bases)) { | ||
| base_dat[,bases[base]] <- as.numeric(base_seq==bases[base]) | ||
| } | ||
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| ## Stretches of N's | ||
| N_rle <- Rle(base_dat[,"N"]) | ||
| N_dat <- data.frame(start=cumsum(runLength(N_rle))[runValue(N_rle)==1], width=runLength(N_rle)[runValue(N_rle)==1]) | ||
| outfile <- paste(OUTDIR, PREFIXES[idx], ".N_run.tsv", sep='') | ||
| write.table(N_dat, file=outfile, col.names=TRUE, row.names=FALSE, sep="\t", quote=FALSE) | ||
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| ## Running mean of bp density for standard bases | ||
| run_k <- 1001 | ||
| run_dat <- base_dat[,c("sample", "position", bases_std)] | ||
| for (base in bases_std) { | ||
| run_dat[,base] <- as.numeric(runmean(Rle(base_dat[,base]), k=run_k, endrule="constant")) | ||
| } | ||
| run_dat <- melt(run_dat, c(1,2)) | ||
| colnames(run_dat)[3] <- "base" | ||
| run_dat$position <- run_dat$position/1000 | ||
| lineplot <- ggplot(run_dat,aes(x=position, y=value, colour=base)) + | ||
| geom_line() + | ||
| theme_classic() + | ||
| theme(panel.border=element_rect(colour="black", fill=NA, size=1)) + | ||
| scale_y_continuous(breaks=c(0,0.25,0.50,0.75,1)) + | ||
| xlab("Position (Kb)") + | ||
| ylab(paste("Base density (running mean k=",run_k,")", sep='')) + | ||
| ggtitle(PREFIXES[idx]) + | ||
| scale_colour_manual(values=base_cols) | ||
| outfile <- paste(OUTDIR, PREFIXES[idx], ".ACTG_density.pdf", sep='') | ||
| ggsave(file=outfile, lineplot, width=18, height=10, units="cm") | ||
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| ## Single base density plots, nucleotide resolution. | ||
| bases_other <- bases[!bases %in% bases_std] | ||
| for (obase in bases_other) { | ||
| plot_dat <- base_dat[,c("sample", "position", obase)] | ||
| colnames(plot_dat)[3] <- "base" | ||
| plot_col <- ifelse(obase=="N", base_cols[["N"]], base_cols[["X"]]) | ||
| lineplot <- ggplot(plot_dat, aes(x=position/1000, y=base)) + | ||
| geom_line(colour=plot_col) + | ||
| theme_classic() + | ||
| theme(legend.position="none", panel.border=element_rect(colour="black", fill=NA, size=1)) + | ||
| scale_y_continuous(breaks=c(0,1), labels=c(0,1)) + | ||
| xlab("Position (Kb)") + | ||
| ylab(paste(obase,"density", sep=' ')) + | ||
| ggtitle(PREFIXES[idx]) | ||
| outfile <- paste(OUTDIR, PREFIXES[idx], ".", obase, "_density.pdf", sep='') | ||
| ggsave(file=outfile, lineplot, width=18, height=10, units="cm") | ||
| } | ||
| } |
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