sklarz-bgu

if(!(all(c("plyr","optparse","tools","magrittr") %in% installed.packages()))) {
    cat("'plyr','optparse','tools','magrittr' are not installed.\nYou must install them for this script to work!\nInstall by running the following commands:\ninstall.packages('plyr')\ninstall.packages('optparse')\ninstall.packages('tools')\ninstall.packages('magrittr')")
}

library(plyr)
library(optparse)
library(tools)
library(magrittr)

sklarz-bgu

library("magrittr")
library("optparse")

args = commandArgs(trailingOnly=TRUE)

option_list = list(
    make_option(c("-d", "--dir"), type="character", default=NULL, 
                help="Directory of fastqc results", metavar="character"),
    make_option(c("-o", "--outdir"), type="character", default=NULL, 
                help="An existing dir in which to create the output files.", metavar="character")

sklarz-bgu

library(magrittr)

colhex2col <- function(colhex) {
    # Convert hex to RGB
    mycol   <- colhex %>% col2rgb()
    # Convert all x11 colors to RGB, adn transform
    colors()                 %>%        # Get X11 colors (hex)
        col2rgb              %>%        # Convert to RGB matrix
        data.frame           %>%        # Convert to data.frame
        setNames(.,colors()) %>%        # Set color names