Nchart.R

#!/usr/bin/env Rscript

library(ggplot2)
library(scales)

args <- commandArgs(TRUE)

if (length(args) < 2) {
  cat("USAGE: Nchart.R out.png lens1 lens2 lens3 ... lensN\n")
} else {

# output prefix
outfile <- args[[1]]

ref_filename <- args[[2]]
ref_name <- ref_filename

query_filenames = tail(args, -2)
query_names <- query_filenames

colors <- rainbow(length(query_filenames))

## Assume the first entry is the reference

cat("Creating Nchart\n")
cat("===============\n")
cat("outfile: ",         outfile, "\n")
cat("ref_filename: ",    ref_filename, "\n")


## Load the reference lens
#############################################################################
ref.data <- read.table(ref_filename, header=FALSE)
names(ref.data) <- c("name","length")
ref.data$length <- sort(as.numeric(ref.data$length),decreasing=TRUE)
genome.length <- max(sum(ref.data$length))
ref.cumsum <- data.frame(NG=cumsum(ref.data$length/genome.length*100),contig.length=ref.data$length,contig.source=ref_name)
ref.cumsum.0 <- rbind(data.frame(NG=c(0),contig.length=max(ref.cumsum$contig.length),contig.source=ref_name),ref.cumsum)

## Now process each query
############################################################################

if (length(query_filenames) > 0)
{
  for (i in seq(length(query_filenames))) {
    filename_query = query_filenames[i]
    name_query = query_names[i]
    cat("query: ", i, " ", filename_query, " ", name_query, "\n")
    
    query.data <- read.table(filename_query, header=FALSE)
    names(query.data) <- c("name","length")
    query.data$length <- sort(as.numeric(query.data$length),decreasing=TRUE)
    query.cumsum <- data.frame(NG=cumsum(query.data$length/genome.length*100),contig.length=query.data$length,contig.source=name_query)
    query.cumsum.0 <- rbind(data.frame(NG=c(0),contig.length=max(query.cumsum$contig.length),contig.source=name_query),query.cumsum)
    ref.cumsum <- rbind(ref.cumsum,query.cumsum)
    ref.cumsum.0 <- rbind(ref.cumsum.0,query.cumsum.0)
  }
}


bp_format<-function(num) {
  if (num > 1000000000) {
    paste(formatC(num/1000000000,format="f",digits=1,big.mark=",",drop0trailing = TRUE)," Gbp",sep="")
  }
  else if (num > 1000000) {
    paste(formatC(num/1000000,format="f",digits=1,big.mark=",",drop0trailing = TRUE)," Mbp",sep="")
  }
  else {
    paste(formatC(num,format="f",big.mark=",",drop0trailing = TRUE), " bp", sep="")
  } 
}

theme_set(theme_bw(base_size = 12) + theme(panel.grid.minor = element_line(colour = NA)))

percent_format <- function(num) {
  paste(num,"%", sep="")
}

cat("make plot: ", outfile, "\n")

png(file=outfile, width=1600,height=1000,res=200)

print(
  ggplot(ref.cumsum.0, aes(x = NG, y = contig.length, color=contig.source)) + 
     #            xlim(0,100) +
    scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x), labels = trans_format("log10", math_format(10^.x)), limits=c(1,genome.length)) + 
    scale_x_continuous(labels=percent_format) +
    geom_path(size=1.5,alpha=0.5) + 
    geom_point(data=ref.cumsum, size=2,alpha=0.5) + 
    labs(x = paste("Percentage of reference (",bp_format(genome.length),")", sep=""),y="Sequence length",colour="Assembly",title="Cumulative sequence length") +
   # scale_color_manual(values=colors) +
    annotation_logticks(sides="lr")
)

dev.off()

}