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123
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1 library(ggplot2)
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2 library(reshape2)
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3
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4 args <- commandArgs(trailingOnly = TRUE)
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5
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6 input.file = args[1] #the data that's get turned into the "SHM overview" table in the html report "data_sum.txt"
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7 plot1.file = args[2]
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8 plot2.file = args[3]
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9 plot3.file = args[4]
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10
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11 dat = read.table(input.file, header=F, sep=",", quote="", stringsAsFactors=F, fill=T)
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12
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13 classes = c("ca", "ca1", "ca2", "cg", "cg1", "cg2", "cg3", "cg4", "cm")
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14 xyz = c("x", "y", "z")
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15
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16 names(dat) = c("info", paste(rep(classes, each=3), xyz, sep="."), paste("un", xyz, sep="."), paste("all", xyz, sep="."))
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17
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