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1 #!/usr/local/R-4.1.2/bin/R
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2
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3
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4 library(dendextend)
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5 library("optparse")
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6 library(reshape2)
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7 library(ape)
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8
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9
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10 #args = commandArgs(trailingOnly=TRUE)
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11
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12 option_list = list(
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13 make_option(c("-f", "--file"), type="character", default=NULL,
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14 help="dataset file name", metavar="character"),
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15 make_option(c("-o", "--out"), type="character", default="out.txt",
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16 help="output file name [default= %default]", metavar="character")
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17 );
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18 opt_parser = OptionParser(option_list=option_list);
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19 opt = parse_args(opt_parser);
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20
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21 if (is.null(opt$file)){
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22 print_help(opt_parser)
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23 stop("At least one argument must be supplied (input file).\n", call.=FALSE)
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24 }
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25
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26 if (is.null(opt$out)){
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27 print_help(opt_parser)
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28 stop("At least one argument must be supplied (out file).\n", call.=FALSE)
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29 }
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30
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31 #svglite(opt$out,width = 31, height = 28)
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32 pdf(opt$out,width = 31,height = 28)
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33
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34 mydata <- read.table(opt$file, header=TRUE,sep="\t", row.names="Gene")
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35
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36 iris <- mydata
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37
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38 #dend_r <- iris %>% dist(method = "man") %>% hclust(method = "ward.D") %>% as.dendrogram %>% ladderize
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39 #dend_r <- iris %>% dist(method = "man") %>% hclust(method = "com") %>% as.dendrogram %>% ladderize
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40
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41 #dend_c <- t(iris) %>% dist(method = "man") %>% hclust(method = "com") %>% as.dendrogram %>% ladderize
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42 #dend_c <- t(iris) %>% dist(method = "man") %>% hclust(method = "ward.D") %>% as.dendrogram %>% ladderize
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43
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44 #dend_c
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45
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46
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47 distance_matrix = t(iris) %>% dist(method = "man")
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48 h = distance_matrix %>% hclust(method = "ward.D")
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49
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50 tree = as.phylo(h)
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51
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52
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53 dend_c = h %>% as.dendrogram
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54
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55
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56 write.tree(tree, file=paste(opt$out, "distance_matrix.hclust.newick", sep="."))
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57
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58 dist_df <- melt(as.matrix(distance_matrix), varnames = c("row", "col"))
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59 write.table(
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60 dist_df,
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61 paste(opt$out, "distance_matrix.txt", sep=".")
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62 )
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63
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64 mat <- as.matrix(t(iris-1))
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65 out <- gplots::heatmap.2(mat,
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66 main = "",
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67 scale="none",
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68 srtCol=NULL,
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69 Rowv = dend_c,
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70 #Colv = dend_r,
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71 key = FALSE,
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72 margins =c(20,20),
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73 trace="row", hline = NA, tracecol = NA
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74 )
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75
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76 write.table(
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77 data.frame(gene = rownames(mat)[out$rowInd]),
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78 paste(opt$out, "rows.csv", sep="."),
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79 row.names = FALSE,
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80 quote = FALSE,
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81 sep = ',')
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82
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83 write.table(
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84 data.frame(gene = colnames(mat)[out$colInd]),
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85 paste(opt$out, "cols.csv", sep="."),
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86 row.names = FALSE,
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87 quote = FALSE,
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88 sep = ',')
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89
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90 dev.off()
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91
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