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0
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1 library(reshape2)
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2
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3 args <- commandArgs(trailingOnly = TRUE)
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4
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5 before.unique.file = args[1]
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6 merged.file = args[2]
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7 outputdir = args[3]
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8 gene.classes = unlist(strsplit(args[4], ","))
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9 hotspot.analysis.sum.file = args[5]
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10 NToverview.file = paste(outputdir, "ntoverview.txt", sep="/")
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11 NTsum.file = paste(outputdir, "ntsum.txt", sep="/")
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12 main.html = "index.html"
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7
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13 empty.region.filter = args[6]
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14
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0
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15
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16 setwd(outputdir)
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17
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18 before.unique = read.table(before.unique.file, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="")
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19 merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="")
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20 hotspot.analysis.sum = read.table(hotspot.analysis.sum.file, header=F, sep=",", fill=T, stringsAsFactors=F, quote="")
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21
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22 #before.unique = before.unique[!grepl("unmatched", before.unique$best_match),]
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23
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7
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24 if(empty.region.filter == "leader"){
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25 before.unique$seq_conc = paste(before.unique$FR1.IMGT.seq, before.unique$CDR1.IMGT.seq, before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq)
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26 } else if(empty.region.filter == "FR1"){
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27 before.unique$seq_conc = paste(before.unique$CDR1.IMGT.seq, before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq)
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28 } else if(empty.region.filter == "CDR1"){
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29 before.unique$seq_conc = paste(before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq)
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30 } else if(empty.region.filter == "FR2"){
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31 before.unique$seq_conc = paste(before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq)
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32 }
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0
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33
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34 IDs = before.unique[,c("Sequence.ID", "seq_conc", "best_match", "Functionality")]
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35 IDs$best_match = as.character(IDs$best_match)
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36
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7
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37 dat = data.frame(table(before.unique$seq_conc))
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38
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39 names(dat) = c("seq_conc", "Freq")
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40
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41 dat$seq_conc = factor(dat$seq_conc)
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42
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43 dat = dat[order(as.character(dat$seq_conc)),]
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44
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45 #writing html from R...
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46 get.bg.color = function(val){
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47 if(val %in% c("TRUE", "FALSE", "T", "F")){ #if its a logical value, give the background a green/red color
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48 return(ifelse(val,"#eafaf1","#f9ebea"))
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49 } else if (!is.na(as.numeric(val))) { #if its a numerical value, give it a grey tint if its >0
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50 return(ifelse(val > 0,"#eaecee","white"))
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51 } else {
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52 return("white")
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53 }
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54 }
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55 td = function(val) {
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56 return(paste("<td bgcolor='", get.bg.color(val), "'>", val, "</td>", sep=""))
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57 }
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58 tr = function(val) {
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59 return(paste(c("<tr>", sapply(val, td), "</tr>"), collapse=""))
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60 }
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61
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62 make.link = function(id, clss, val) {
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63 paste("<a href='", clss, "_", id, ".html'>", val, "</a>", sep="")
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64 }
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65 tbl = function(df) {
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66 res = "<table border='1'>"
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67 for(i in 1:nrow(df)){
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68 res = paste(res, tr(df[i,]), sep="")
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69 }
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70 res = paste(res, "</table>")
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71 }
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72
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73 cat("<table border='1' class='pure-table pure-table-striped'>", file=main.html, append=F)
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7
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74
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75 if(empty.region.filter == "leader"){
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76 cat("<caption>FR1+CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T)
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77 } else if(empty.region.filter == "FR1"){
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78 cat("<caption>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T)
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79 } else if(empty.region.filter == "CDR1"){
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80 cat("<caption>FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T)
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81 } else if(empty.region.filter == "FR2"){
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82 cat("<caption>CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T)
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83 }
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84
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0
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85 cat("<tr>", file=main.html, append=T)
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86 cat("<th>Sequence</th><th>Functionality</th><th>ca1</th><th>ca2</th><th>cg1</th><th>cg2</th><th>cg3</th><th>cg4</th><th>cm</th><th>un</th>", file=main.html, append=T)
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87 cat("<th>total CA</th><th>total CG</th><th>number of subclasses</th><th>present in both Ca and Cg</th><th>Ca1+Ca2</th>", file=main.html, append=T)
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88 cat("<th>Cg1+Cg2</th><th>Cg1+Cg3</th><th>Cg1+Cg4</th><th>Cg2+Cg3</th><th>Cg2+Cg4</th><th>Cg3+Cg4</th>", file=main.html, append=T)
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89 cat("<th>Cg1+Cg2+Cg3</th><th>Cg2+Cg3+Cg4</th><th>Cg1+Cg2+Cg4</th><th>Cg1+Cg3+Cg4</th><th>Cg1+Cg2+Cg3+Cg4</th>", file=main.html, append=T)
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90 cat("</tr>", file=main.html, append=T)
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91
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92
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93
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94 single.sequences=0 #sequence only found once, skipped
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95 in.multiple=0 #same sequence across multiple subclasses
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96 multiple.in.one=0 #same sequence multiple times in one subclass
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97 unmatched=0 #all of the sequences are unmatched
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98 some.unmatched=0 #one or more sequences in a clone are unmatched
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99 matched=0 #should be the same als matched sequences
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100
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101 sequence.id.page="by_id.html"
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102
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103 for(i in 1:nrow(dat)){
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104
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105 ca1 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGA1", IDs$best_match),]
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106 ca2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGA2", IDs$best_match),]
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107
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108 cg1 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGG1", IDs$best_match),]
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109 cg2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGG2", IDs$best_match),]
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110 cg3 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGG3", IDs$best_match),]
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111 cg4 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGG4", IDs$best_match),]
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112
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113 cm = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGM", IDs$best_match),]
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114
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115 un = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^unmatched", IDs$best_match),]
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116 allc = rbind(ca1, ca2, cg1, cg2, cg3, cg4, cm, un)
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117
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118 ca1.n = nrow(ca1)
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119 ca2.n = nrow(ca2)
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120
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121 cg1.n = nrow(cg1)
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122 cg2.n = nrow(cg2)
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123 cg3.n = nrow(cg3)
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124 cg4.n = nrow(cg4)
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125
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126 cm.n = nrow(cm)
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127
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128 un.n = nrow(un)
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129
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130 classes = c(ca1.n, ca2.n, cg1.n, cg2.n, cg3.n, cg4.n, cm.n, un.n)
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131
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132 classes.sum = sum(classes)
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133
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134 if(classes.sum == 1){
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135 single.sequences = single.sequences + 1
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136 next
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137 }
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138
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139 if(un.n == classes.sum){
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140 unmatched = unmatched + 1
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141 next
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142 }
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143
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144 in.classes = sum(classes > 0)
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145
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146 matched = matched + in.classes #count in how many subclasses the sequence occurs.
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147
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148 if(any(classes == classes.sum)){
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149 multiple.in.one = multiple.in.one + 1
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150 } else if (un.n > 0) {
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151 some.unmatched = some.unmatched + 1
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152 } else {
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153 in.multiple = in.multiple + 1
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154 }
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155
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156 id = as.numeric(dat[i,"seq_conc"])
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157
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158 functionality = paste(unique(allc[,"Functionality"]), collapse=",")
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159
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160 by.id.row = c()
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161
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162 if(ca1.n > 0){
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163 cat(tbl(ca1), file=paste("IGA1_", id, ".html", sep=""))
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164 }
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165
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166 if(ca2.n > 0){
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167 cat(tbl(ca2), file=paste("IGA2_", id, ".html", sep=""))
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168 }
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169
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170 if(cg1.n > 0){
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171 cat(tbl(cg1), file=paste("IGG1_", id, ".html", sep=""))
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172 }
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173
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174 if(cg2.n > 0){
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175 cat(tbl(cg2), file=paste("IGG2_", id, ".html", sep=""))
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176 }
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177
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178 if(cg3.n > 0){
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179 cat(tbl(cg3), file=paste("IGG3_", id, ".html", sep=""))
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180 }
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181
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182 if(cg4.n > 0){
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183 cat(tbl(cg4), file=paste("IGG4_", id, ".html", sep=""))
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184 }
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185
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186 if(cm.n > 0){
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187 cat(tbl(cm), file=paste("IGM_", id, ".html", sep=""))
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188 }
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189
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190 if(un.n > 0){
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191 cat(tbl(un), file=paste("un_", id, ".html", sep=""))
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192 }
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193
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194 ca1.html = make.link(id, "IGA1", ca1.n)
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195 ca2.html = make.link(id, "IGA2", ca2.n)
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196
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197 cg1.html = make.link(id, "IGG1", cg1.n)
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198 cg2.html = make.link(id, "IGG2", cg2.n)
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199 cg3.html = make.link(id, "IGG3", cg3.n)
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200 cg4.html = make.link(id, "IGG4", cg4.n)
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201
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202 cm.html = make.link(id, "IGM", cm.n)
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203
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204 un.html = make.link(id, "un", un.n)
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205
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206 #extra columns
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207 ca.n = ca1.n + ca2.n
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208
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209 cg.n = cg1.n + cg2.n + cg3.n + cg4.n
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210
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211 #in.classes
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212
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213 in.ca.cg = (ca.n > 0 & cg.n > 0)
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214
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215 in.ca1.ca2 = (ca1.n > 0 & ca2.n > 0)
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216
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217 in.cg1.cg2 = (cg1.n > 0 & cg2.n > 0)
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218 in.cg1.cg3 = (cg1.n > 0 & cg3.n > 0)
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219 in.cg1.cg4 = (cg1.n > 0 & cg4.n > 0)
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220 in.cg2.cg3 = (cg2.n > 0 & cg3.n > 0)
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221 in.cg2.cg4 = (cg2.n > 0 & cg4.n > 0)
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222 in.cg3.cg4 = (cg3.n > 0 & cg4.n > 0)
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223
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224 in.cg1.cg2.cg3 = (cg1.n > 0 & cg2.n > 0 & cg3.n > 0)
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225 in.cg2.cg3.cg4 = (cg2.n > 0 & cg3.n > 0 & cg4.n > 0)
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226 in.cg1.cg2.cg4 = (cg1.n > 0 & cg2.n > 0 & cg4.n > 0)
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227 in.cg1.cg3.cg4 = (cg1.n > 0 & cg3.n > 0 & cg4.n > 0)
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228
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229 in.cg.all = (cg1.n > 0 & cg2.n > 0 & cg3.n > 0 & cg4.n > 0)
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230
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231
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232
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233
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234 #rw = c(as.character(dat[i,"seq_conc"]), functionality, ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html, un.html)
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235 rw = c(as.character(dat[i,"seq_conc"]), functionality, ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html, un.html)
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236 rw = c(rw, ca.n, cg.n, in.classes, in.ca.cg, in.ca1.ca2, in.cg1.cg2, in.cg1.cg3, in.cg1.cg4, in.cg2.cg3, in.cg2.cg4, in.cg3.cg4, in.cg1.cg2.cg3, in.cg2.cg3.cg4, in.cg1.cg2.cg4, in.cg1.cg3.cg4, in.cg.all)
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237
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238 cat(tr(rw), file=main.html, append=T)
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239
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240
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241 for(i in 1:nrow(allc)){ #generate html by id
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242 html = make.link(id, allc[i,"best_match"], allc[i,"Sequence.ID"])
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243 cat(paste(html, "<br />"), file=sequence.id.page, append=T)
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244 }
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245 }
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246
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247 cat("</table>", file=main.html, append=T)
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248
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249 print(paste("Single sequences:", single.sequences))
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250 print(paste("Sequences in multiple subclasses:", in.multiple))
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251 print(paste("Multiple sequences in one subclass:", multiple.in.one))
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252 print(paste("Matched with unmatched:", some.unmatched))
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253 print(paste("Count that should match 'matched' sequences:", matched))
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254
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255 #ACGT overview
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256
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7
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257 #NToverview = merged[!grepl("^unmatched", merged$best_match),]
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258 NToverview = merged
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0
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259
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7
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260 if(empty.region.filter == "leader"){
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261 NToverview$seq = paste(NToverview$FR1.IMGT.seq, NToverview$CDR1.IMGT.seq, NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq)
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262 } else if(empty.region.filter == "FR1"){
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263 NToverview$seq = paste(NToverview$CDR1.IMGT.seq, NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq)
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264 } else if(empty.region.filter == "CDR1"){
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265 NToverview$seq = paste(NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq)
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266 } else if(empty.region.filter == "FR2"){
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267 NToverview$seq = paste(NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq)
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268 }
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0
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269
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270 NToverview$A = nchar(gsub("[^Aa]", "", NToverview$seq))
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271 NToverview$C = nchar(gsub("[^Cc]", "", NToverview$seq))
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272 NToverview$G = nchar(gsub("[^Gg]", "", NToverview$seq))
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273 NToverview$T = nchar(gsub("[^Tt]", "", NToverview$seq))
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274
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275 #Nsum = data.frame(Sequence.ID="-", best_match="Sum", seq="-", A = sum(NToverview$A), C = sum(NToverview$C), G = sum(NToverview$G), T = sum(NToverview$T))
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276
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277 #NToverview = rbind(NToverview, NTsum)
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278
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279 NTresult = data.frame(nt=c("A", "C", "T", "G"))
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280
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281 for(clazz in gene.classes){
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8
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282 print(paste("class:", clazz))
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283 NToverview.sub = NToverview[grepl(paste("^", clazz, sep=""), NToverview$best_match),]
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8
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284 print(paste("nrow:", nrow(NToverview.sub)))
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285 new.col.x = c(sum(NToverview.sub$A), sum(NToverview.sub$C), sum(NToverview.sub$T), sum(NToverview.sub$G))
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286 new.col.y = sum(new.col.x)
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287 new.col.z = round(new.col.x / new.col.y * 100, 2)
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288
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289 tmp = names(NTresult)
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290 NTresult = cbind(NTresult, data.frame(new.col.x, new.col.y, new.col.z))
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291 names(NTresult) = c(tmp, paste(clazz, c("x", "y", "z"), sep=""))
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292 }
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293
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294 write.table(NToverview[,c("Sequence.ID", "best_match", "seq", "A", "C", "G", "T")], NToverview.file, quote=F, sep="\t", row.names=F, col.names=T)
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295
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296 NToverview = NToverview[!grepl("unmatched", NToverview$best_match),]
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297
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298 new.col.x = c(sum(NToverview$A), sum(NToverview$C), sum(NToverview$T), sum(NToverview$G))
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299 new.col.y = sum(new.col.x)
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300 new.col.z = round(new.col.x / new.col.y * 100, 2)
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301
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302 tmp = names(NTresult)
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303 NTresult = cbind(NTresult, data.frame(new.col.x, new.col.y, new.col.z))
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304 names(NTresult) = c(tmp, paste("all", c("x", "y", "z"), sep=""))
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305
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306 names(hotspot.analysis.sum) = names(NTresult)
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307
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308 hotspot.analysis.sum = rbind(hotspot.analysis.sum, NTresult)
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309
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310 write.table(hotspot.analysis.sum, hotspot.analysis.sum.file, quote=F, sep=",", row.names=F, col.names=F, na="0")
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311
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312
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313
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314
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315
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316
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317
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318
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319
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320
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321
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322
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323
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324
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325
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326
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327
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328
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329
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330
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331
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332
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333
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334
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335
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336
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338
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339
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340
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