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0
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1 args <- commandArgs(trailingOnly = TRUE)
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2
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3 input = args[1]
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4
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4 genes = unlist(strsplit(args[2], ","))
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0
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5 outputdir = args[3]
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22
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6 print(args[4])
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7 include_fr1 = ifelse(args[4] == "yes", T, F)
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0
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8 setwd(outputdir)
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9
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10 dat = read.table(input, header=T, sep="\t", fill=T, stringsAsFactors=F)
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11
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12 if(length(dat$Sequence.ID) == 0){
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4
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13 setwd(outputdir)
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14 result = data.frame(x = rep(0, 5), y = rep(0, 5), z = rep(NA, 5))
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15 row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C G (%)")
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16 write.table(x=result, file="mutations.txt", sep=",",quote=F,row.names=T,col.names=F)
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17 transitionTable = data.frame(A=rep(0, 4),C=rep(0, 4),G=rep(0, 4),T=rep(0, 4))
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18 row.names(transitionTable) = c("A", "C", "G", "T")
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19 transitionTable["A","A"] = NA
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20 transitionTable["C","C"] = NA
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21 transitionTable["G","G"] = NA
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22 transitionTable["T","T"] = NA
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23 write.table(x=transitionTable, file="transitions.txt", sep=",",quote=F,row.names=T,col.names=NA)
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24 cat("0", file="n.txt")
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25 stop("No data")
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0
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26 }
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27
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28
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29
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30 cleanup_columns = c("FR1.IMGT.c.a",
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31 "FR2.IMGT.g.t",
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32 "CDR1.IMGT.Nb.of.nucleotides",
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33 "CDR2.IMGT.t.a",
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34 "FR1.IMGT.c.g",
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35 "CDR1.IMGT.c.t",
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36 "FR2.IMGT.a.c",
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37 "FR2.IMGT.Nb.of.mutations",
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38 "FR2.IMGT.g.c",
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39 "FR2.IMGT.a.g",
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40 "FR3.IMGT.t.a",
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41 "FR3.IMGT.t.c",
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42 "FR2.IMGT.g.a",
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43 "FR3.IMGT.c.g",
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44 "FR1.IMGT.Nb.of.mutations",
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45 "CDR1.IMGT.g.a",
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46 "CDR1.IMGT.t.g",
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47 "CDR1.IMGT.g.c",
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48 "CDR2.IMGT.Nb.of.nucleotides",
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49 "FR2.IMGT.a.t",
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50 "CDR1.IMGT.Nb.of.mutations",
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51 "CDR1.IMGT.a.g",
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52 "FR3.IMGT.a.c",
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53 "FR1.IMGT.g.a",
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54 "FR3.IMGT.a.g",
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55 "FR1.IMGT.a.t",
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56 "CDR2.IMGT.a.g",
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57 "CDR2.IMGT.Nb.of.mutations",
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58 "CDR2.IMGT.g.t",
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59 "CDR2.IMGT.a.c",
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60 "CDR1.IMGT.t.c",
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61 "FR3.IMGT.g.c",
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62 "FR1.IMGT.g.t",
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63 "FR3.IMGT.g.t",
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64 "CDR1.IMGT.a.t",
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65 "FR1.IMGT.a.g",
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66 "FR3.IMGT.a.t",
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67 "FR3.IMGT.Nb.of.nucleotides",
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68 "FR2.IMGT.t.c",
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69 "CDR2.IMGT.g.a",
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70 "FR2.IMGT.t.a",
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71 "CDR1.IMGT.t.a",
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72 "FR2.IMGT.t.g",
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73 "FR3.IMGT.t.g",
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74 "FR2.IMGT.Nb.of.nucleotides",
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75 "FR1.IMGT.t.a",
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76 "FR1.IMGT.t.g",
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77 "FR3.IMGT.c.t",
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78 "FR1.IMGT.t.c",
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79 "CDR2.IMGT.a.t",
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80 "FR2.IMGT.c.t",
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81 "CDR1.IMGT.g.t",
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82 "CDR2.IMGT.t.g",
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83 "FR1.IMGT.Nb.of.nucleotides",
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84 "CDR1.IMGT.c.g",
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85 "CDR2.IMGT.t.c",
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86 "FR3.IMGT.g.a",
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87 "CDR1.IMGT.a.c",
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88 "FR2.IMGT.c.a",
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89 "FR3.IMGT.Nb.of.mutations",
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90 "FR2.IMGT.c.g",
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91 "CDR2.IMGT.g.c",
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92 "FR1.IMGT.g.c",
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93 "CDR2.IMGT.c.t",
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94 "FR3.IMGT.c.a",
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95 "CDR1.IMGT.c.a",
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96 "CDR2.IMGT.c.g",
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97 "CDR2.IMGT.c.a",
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98 "FR1.IMGT.c.t")
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99
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100 for(col in cleanup_columns){
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101 dat[,col] = gsub("\\(.*\\)", "", dat[,col])
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102 #dat[dat[,col] == "",] = "0"
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103 dat[,col] = as.numeric(dat[,col])
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104 dat[is.na(dat[,col]),] = 0
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105 }
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106
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22
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107 regions = c("FR1", "CDR1", "FR2", "CDR2", "FR3")
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108 if(!include_fr1){
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109 regions = c("CDR1", "FR2", "CDR2", "FR3")
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110 }
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0
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111
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22
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112 sum_by_row = function(x, columns) { sum(as.numeric(x[columns]), na.rm=T) }
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0
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113
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22
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114 VRegionMutations_columns = paste(regions, ".IMGT.Nb.of.mutations", sep="")
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115 dat$VRegionMutations = apply(dat, FUN=sum_by_row, 1, columns=VRegionMutations_columns)
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116
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117 VRegionNucleotides_columns = paste(regions, ".IMGT.Nb.of.nucleotides", sep="")
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118 dat$VRegionNucleotides = apply(dat, FUN=sum_by_row, 1, columns=VRegionNucleotides_columns)
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119
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120 transitionMutations_columns = paste(rep(regions, each=4), c(".IMGT.a.g", ".IMGT.g.a", ".IMGT.c.t", ".IMGT.t.c"), sep="")
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121 dat$transitionMutations = apply(dat, FUN=sum_by_row, 1, columns=transitionMutations_columns)
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122
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123 transversionMutations_columns = paste(rep(regions, each=8), c(".IMGT.a.c",".IMGT.c.a",".IMGT.a.t",".IMGT.t.a",".IMGT.g.c",".IMGT.c.g",".IMGT.g.t",".IMGT.t.g"), sep="")
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124 dat$transversionMutations = apply(dat, FUN=sum_by_row, 1, columns=transversionMutations_columns)
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0
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125
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126
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22
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127 transitionMutationsAtGC_columns = paste(rep(regions, each=2), c(".IMGT.g.a",".IMGT.c.t"), sep="")
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128 dat$transitionMutationsAtGC = apply(dat, FUN=sum_by_row, 1, columns=transitionMutationsAtGC_columns)
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0
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129
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22
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130 totalMutationsAtGC_columns = paste(rep(regions, each=6), c(".IMGT.g.a",".IMGT.c.t",".IMGT.c.a",".IMGT.g.c",".IMGT.c.g",".IMGT.g.t"), sep="")
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131 dat$totalMutationsAtGC = apply(dat, FUN=sum_by_row, 1, columns=totalMutationsAtGC_columns)
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0
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132
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24
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133 FRRegions = regions[grepl("FR", regions)]
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134 CDRRegions = regions[grepl("CDR", regions)]
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135
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136 FR_silentMutations_columns = paste(FRRegions, ".IMGT.Nb.of.silent.mutations", sep="")
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137 dat$silentMutationsFR = apply(dat, FUN=sum_by_row, 1, columns=FR_silentMutations_columns)
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23
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138
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24
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139 CDR_silentMutations_columns = paste(CDRRegions, ".IMGT.Nb.of.silent.mutations", sep="")
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140 dat$silentMutationsCDR = apply(dat, FUN=sum_by_row, 1, columns=CDR_silentMutations_columns)
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141
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142 FR_nonSilentMutations_columns = paste(FRRegions, ".IMGT.Nb.of.nonsilent.mutations", sep="")
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143 dat$nonSilentMutationsFR = apply(dat, FUN=sum_by_row, 1, columns=FR_nonSilentMutations_columns)
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144
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145 CDR_nonSilentMutations_columns = paste(CDRRegions, ".IMGT.Nb.of.nonsilent.mutations", sep="")
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146 dat$nonSilentMutationsCDR = apply(dat, FUN=sum_by_row, 1, columns=CDR_nonSilentMutations_columns)
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0
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147
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148
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4
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149 setwd(outputdir)
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150
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26
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151 nts = c("a", "c", "g", "t")
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22
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152 zeros=rep(0, 4)
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24
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153 matrx = matrix(data = 0, ncol=((length(genes) + 1) * 3),nrow=7)
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4
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154 for(i in 1:length(genes)){
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155 gene = genes[i]
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156 tmp = dat[grepl(paste(".*", gene, ".*", sep=""), dat$best_match),]
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157 if(gene == "."){
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158 tmp = dat
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159 }
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160 j = i - 1
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161 x = (j * 3) + 1
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162 y = (j * 3) + 2
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163 z = (j * 3) + 3
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164 matrx[1,x] = sum(tmp$VRegionMutations)
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165 matrx[1,y] = sum(tmp$VRegionNucleotides)
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166 matrx[1,z] = round(matrx[1,x] / matrx[1,y] * 100, digits=1)
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167 matrx[2,x] = sum(tmp$transitionMutations)
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168 matrx[2,y] = sum(tmp$VRegionMutations)
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169 matrx[2,z] = round(matrx[2,x] / matrx[2,y] * 100, digits=1)
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170 matrx[3,x] = sum(tmp$transversionMutations)
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171 matrx[3,y] = sum(tmp$VRegionMutations)
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172 matrx[3,z] = round(matrx[3,x] / matrx[3,y] * 100, digits=1)
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173 matrx[4,x] = sum(tmp$transitionMutationsAtGC)
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174 matrx[4,y] = sum(tmp$totalMutationsAtGC)
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175 matrx[4,z] = round(matrx[4,x] / matrx[4,y] * 100, digits=1)
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176 matrx[5,x] = sum(tmp$totalMutationsAtGC)
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177 matrx[5,y] = sum(tmp$VRegionMutations)
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178 matrx[5,z] = round(matrx[5,x] / matrx[5,y] * 100, digits=1)
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25
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179 matrx[6,x] = sum(tmp$nonSilentMutationsFR)
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180 matrx[6,y] = sum(tmp$silentMutationsFR)
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181 matrx[6,z] = round(matrx[6,x] / matrx[6,y], digits=1)
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182 matrx[7,x] = sum(tmp$nonSilentMutationsCDR)
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183 matrx[7,y] = sum(tmp$silentMutationsCDR)
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184 matrx[7,z] = round(matrx[7,x] / matrx[7,y], digits=1)
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23
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185
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4
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186
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22
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187 transitionTable = data.frame(A=zeros,C=zeros,G=zeros,T=zeros)
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4
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188 row.names(transitionTable) = c("A", "C", "G", "T")
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189 transitionTable["A","A"] = NA
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190 transitionTable["C","C"] = NA
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191 transitionTable["G","G"] = NA
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192 transitionTable["T","T"] = NA
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22
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193
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194 if(nrow(tmp) > 0){
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195 for(nt1 in nts){
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196 for(nt2 in nts){
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197 if(nt1 == nt2){
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198 next
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199 }
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200 NT1 = LETTERS[letters == nt1]
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201 NT2 = LETTERS[letters == nt2]
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202 FR1 = paste("FR1.IMGT.", nt1, ".", nt2, sep="")
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203 CDR1 = paste("CDR1.IMGT.", nt1, ".", nt2, sep="")
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204 FR2 = paste("FR2.IMGT.", nt1, ".", nt2, sep="")
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205 CDR2 = paste("CDR2.IMGT.", nt1, ".", nt2, sep="")
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206 FR3 = paste("FR3.IMGT.", nt1, ".", nt2, sep="")
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207 if(include_fr1){
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208 transitionTable[NT1,NT2] = sum(tmp[,c(FR1, CDR1, FR2, CDR2, FR3)])
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209 } else {
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210 transitionTable[NT1,NT2] = sum(tmp[,c(CDR1, FR2, CDR2, FR3)])
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211 }
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212 }
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213 }
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214 }
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4
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215
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216
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217 write.table(x=transitionTable, file=paste("transitions_", gene ,".txt", sep=""), sep=",",quote=F,row.names=T,col.names=NA)
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218 write.table(x=tmp[,c("Sequence.ID", "best_match", "chunk_hit_percentage", "nt_hit_percentage", "start_locations")], file=paste("matched_", gene ,".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
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219
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220 cat(matrx[1,x], file=paste(gene, "_value.txt" ,sep=""))
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221 cat(length(tmp$Sequence.ID), file=paste(gene, "_n.txt" ,sep=""))
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222 }
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223
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224 #again for all of the data
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225 tmp = dat
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226 j = i
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227 x = (j * 3) + 1
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228 y = (j * 3) + 2
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229 z = (j * 3) + 3
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230 matrx[1,x] = sum(tmp$VRegionMutations)
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231 matrx[1,y] = sum(tmp$VRegionNucleotides)
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232 matrx[1,z] = round(matrx[1,x] / matrx[1,y] * 100, digits=1)
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233 matrx[2,x] = sum(tmp$transitionMutations)
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234 matrx[2,y] = sum(tmp$VRegionMutations)
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235 matrx[2,z] = round(matrx[2,x] / matrx[2,y] * 100, digits=1)
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236 matrx[3,x] = sum(tmp$transversionMutations)
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237 matrx[3,y] = sum(tmp$VRegionMutations)
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238 matrx[3,z] = round(matrx[3,x] / matrx[3,y] * 100, digits=1)
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239 matrx[4,x] = sum(tmp$transitionMutationsAtGC)
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240 matrx[4,y] = sum(tmp$totalMutationsAtGC)
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241 matrx[4,z] = round(matrx[4,x] / matrx[4,y] * 100, digits=1)
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242 matrx[5,x] = sum(tmp$totalMutationsAtGC)
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243 matrx[5,y] = sum(tmp$VRegionMutations)
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244 matrx[5,z] = round(matrx[5,x] / matrx[5,y] * 100, digits=1)
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25
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245 matrx[6,x] = sum(tmp$nonSilentMutationsFR)
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246 matrx[6,y] = sum(tmp$silentMutationsFR)
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247 matrx[6,z] = round(matrx[6,x] / matrx[6,y], digits=1)
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248 matrx[7,x] = sum(tmp$nonSilentMutationsCDR)
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249 matrx[7,y] = sum(tmp$silentMutationsCDR)
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250 matrx[7,z] = round(matrx[7,x] / matrx[7,y], digits=1)
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0
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251
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252 transitionTable = data.frame(A=1:4,C=1:4,G=1:4,T=1:4)
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253 row.names(transitionTable) = c("A", "C", "G", "T")
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254 transitionTable["A","A"] = NA
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255 transitionTable["C","C"] = NA
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256 transitionTable["G","G"] = NA
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257 transitionTable["T","T"] = NA
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258
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259
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260 for(nt1 in nts){
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4
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261 for(nt2 in nts){
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262 if(nt1 == nt2){
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263 next
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264 }
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265 NT1 = LETTERS[letters == nt1]
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266 NT2 = LETTERS[letters == nt2]
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267 FR1 = paste("FR1.IMGT.", nt1, ".", nt2, sep="")
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268 CDR1 = paste("CDR1.IMGT.", nt1, ".", nt2, sep="")
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269 FR2 = paste("FR2.IMGT.", nt1, ".", nt2, sep="")
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270 CDR2 = paste("CDR2.IMGT.", nt1, ".", nt2, sep="")
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271 FR3 = paste("FR3.IMGT.", nt1, ".", nt2, sep="")
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22
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272 if(include_fr1){
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273 transitionTable[NT1,NT2] = sum(tmp[,c(FR1, CDR1, FR2, CDR2, FR3)])
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274 } else {
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275 transitionTable[NT1,NT2] = sum(tmp[,c(CDR1, FR2, CDR2, FR3)])
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276 }
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4
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277 }
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278 }
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279 write.table(x=transitionTable, file="transitions.txt", sep=",",quote=F,row.names=T,col.names=NA)
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280 write.table(x=tmp[,c("Sequence.ID", "best_match", "chunk_hit_percentage", "nt_hit_percentage", "start_locations")], file="matched_all.txt", sep="\t",quote=F,row.names=F,col.names=T)
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281 cat(matrx[1,x], file="total_value.txt")
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282 cat(length(tmp$Sequence.ID), file="total_n.txt")
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283
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284
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285
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286 result = data.frame(matrx)
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25
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287 row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C.G (%)", "FR S/R (ratio)", "CDR S/R (ratio)")
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4
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288
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289 write.table(x=result, file="mutations.txt", sep=",",quote=F,row.names=T,col.names=F)
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290
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291
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292 if (!("ggplot2" %in% rownames(installed.packages()))) {
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293 install.packages("ggplot2", repos="http://cran.xl-mirror.nl/")
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294 }
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295 library(ggplot2)
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296
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297 genesForPlot = gsub("[0-9]", "", dat$best_match)
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298 genesForPlot = data.frame(table(genesForPlot))
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299 colnames(genesForPlot) = c("Gene","Freq")
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300 genesForPlot$label = paste(genesForPlot$Gene, "-", genesForPlot$Freq)
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|
26
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301 write.table(genesForPlot, "all.txt", sep="\t",quote=F,row.names=F,col.names=T)
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302
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4
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303
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304 pc = ggplot(genesForPlot, aes(x = factor(1), y=Freq, fill=label))
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305 pc = pc + geom_bar(width = 1, stat = "identity")
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306 pc = pc + coord_polar(theta="y")
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26
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307 pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("Classes", "( n =", sum(genesForPlot$Freq), ")"))
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4
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308
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309 png(filename="all.png")
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310 pc
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311 dev.off()
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312
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313
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314 #blegh
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315 genesForPlot = dat[grepl("ca", dat$best_match),]$best_match
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316 if(length(genesForPlot) > 0){
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317 genesForPlot = data.frame(table(genesForPlot))
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318 colnames(genesForPlot) = c("Gene","Freq")
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319 genesForPlot$label = paste(genesForPlot$Gene, "-", genesForPlot$Freq)
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320
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321 pc = ggplot(genesForPlot, aes(x = factor(1), y=Freq, fill=label))
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322 pc = pc + geom_bar(width = 1, stat = "identity")
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323 pc = pc + coord_polar(theta="y")
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26
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324 pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("IgA subclasses", "( n =", sum(genesForPlot$Freq), ")"))
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325 write.table(genesForPlot, "ca.txt", sep="\t",quote=F,row.names=F,col.names=T)
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4
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326
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327 png(filename="ca.png")
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328 print(pc)
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329 dev.off()
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0
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330 }
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331
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4
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332 genesForPlot = dat[grepl("cg", dat$best_match),]$best_match
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333 if(length(genesForPlot) > 0){
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334 genesForPlot = data.frame(table(genesForPlot))
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335 colnames(genesForPlot) = c("Gene","Freq")
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336 genesForPlot$label = paste(genesForPlot$Gene, "-", genesForPlot$Freq)
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337
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338 pc = ggplot(genesForPlot, aes(x = factor(1), y=Freq, fill=label))
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339 pc = pc + geom_bar(width = 1, stat = "identity")
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340 pc = pc + coord_polar(theta="y")
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26
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341 pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("IgG subclasses", "( n =", sum(genesForPlot$Freq), ")"))
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342 write.table(genesForPlot, "cg.txt", sep="\t",quote=F,row.names=F,col.names=T)
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0
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343
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4
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344 png(filename="cg.png")
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345 print(pc)
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346 dev.off()
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347 }
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22
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348
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349 dat$percentage_mutations = round(dat$VRegionMutations / dat$VRegionNucleotides * 100, 2)
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350
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26
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351 p = ggplot(dat, aes(best_match, percentage_mutations))
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23
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352 p = p + geom_boxplot(aes(middle=mean(percentage_mutations)), alpha=0.1, outlier.shape = NA) + geom_point(aes(colour=best_match), position="jitter")
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22
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353 p = p + xlab("Subclass") + ylab("Frequency") + ggtitle("Frequency scatter plot")
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26
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354 write.table(dat[,c("Sequence.ID", "best_match", "VRegionMutations", "VRegionNucleotides", "percentage_mutations")], "scatter.txt", sep="\t",quote=F,row.names=F,col.names=T)
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355
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22
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356
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357 png(filename="scatter.png")
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358 print(p)
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359 dev.off()
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360
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361
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362
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363
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364
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365
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366
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367
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368
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369
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370
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371
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372
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373
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374
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375
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376
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377
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378
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379
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380
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381
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382
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383
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384
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385
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386
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387
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388
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389
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390
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391
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