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1 #!/usr/bin/R
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2
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3
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4 library(micropan)
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5 library(dendextend)
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6 library("optparse")
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7
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8
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9 option_list = list(
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10 make_option(c("-f", "--file"), type="character", default=NULL,
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11 help="dataset file name", metavar="character"),
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12 make_option(c("-o", "--out"), type="character", default="out.txt",
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13 help="output file name [default= %default]", metavar="character"),
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14 make_option(c("-a", "--alpha"), type="character", default="heaps.tsv",
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15 help="Heaps output file name [default= %default]", metavar="character"),
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16 make_option(c("-p", "--pdf"), type="character", default="out.pdf",
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17 help="PDF output file name [default= %default]", metavar="character")
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18 );
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19 opt_parser = OptionParser(option_list=option_list);
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20 opt = parse_args(opt_parser);
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21
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22 if (is.null(opt$file)){
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23 print_help(opt_parser)
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24 stop("At least one argument must be supplied (input file).\n", call.=FALSE)
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25 }
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26
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27 if (is.null(opt$out)){
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28 print_help(opt_parser)
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29 stop("At least one argument must be supplied (out file).\n", call.=FALSE)
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30 }
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31 if (is.null(opt$alpha)){
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32 print_help(opt_parser)
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33 stop("At least one argument must be supplied (out file).\n", call.=FALSE)
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34 }
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35 if (is.null(opt$pdf)){
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36 print_help(opt_parser)
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37 stop("At least one argument must be supplied (out file).\n", call.=FALSE)
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38 }
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39
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40
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41 # Loading a pan-matrix in this package
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42 #data(xmpl.panmat)
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43
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44 mydata <- read.table(opt$file, header=TRUE,sep="\t", row.names="Gene")
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45 tmydata<-t(mydata)
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46 #xmpl.panmat
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47
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48 rarefaction = rarefaction(tmydata, n.perm = 100)
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49 write.table(
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50 rarefaction,
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51 opt$out,
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52 row.names = FALSE,
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53 quote = FALSE,
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54 sep = '\t')
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55
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56
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57 # Estimating population openness
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58 h.est <- heaps(tmydata, n.perm = 100)
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59 write.table(
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60 h.est,
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61 opt$alpha,
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62 row.names = TRUE,
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63 quote = FALSE,
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64 sep = '\t')
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65
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66 # If alpha < 1 it indicates an open pan-genome
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67
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68 pdf(opt$pdf)
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69
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70 library(ggplot2)
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71 library(tidyr)
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72 rarefaction %>%
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73 gather(key = "Permutation", value = "Clusters", -Genome) %>%
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74 ggplot(aes(x = Genome, y = Clusters, group = Permutation)) +
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75 geom_point() +
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76 stat_summary(aes(y = Clusters,group=1), fun=mean, colour="red", geom="line",group=1)
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