| 53 | 1 library(data.table) | 
|  | 2 library(ggplot2) | 
|  | 3 | 
|  | 4 args <- commandArgs(trailingOnly = TRUE) | 
|  | 5 | 
|  | 6 input = args[1] | 
|  | 7 genes = unlist(strsplit(args[2], ",")) | 
|  | 8 outputdir = args[3] | 
|  | 9 print(args[4]) | 
|  | 10 include_fr1 = ifelse(args[4] == "yes", T, F) | 
|  | 11 setwd(outputdir) | 
|  | 12 | 
|  | 13 dat = read.table(input, header=T, sep="\t", fill=T, stringsAsFactors=F) | 
|  | 14 | 
|  | 15 if(length(dat$Sequence.ID) == 0){ | 
|  | 16   setwd(outputdir) | 
|  | 17   result = data.frame(x = rep(0, 5), y = rep(0, 5), z = rep(NA, 5)) | 
|  | 18   row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C G (%)") | 
|  | 19   write.table(x=result, file="mutations.txt", sep=",",quote=F,row.names=T,col.names=F) | 
|  | 20   transitionTable = data.frame(A=rep(0, 4),C=rep(0, 4),G=rep(0, 4),T=rep(0, 4)) | 
|  | 21   row.names(transitionTable) = c("A", "C", "G", "T") | 
|  | 22   transitionTable["A","A"] = NA | 
|  | 23   transitionTable["C","C"] = NA | 
|  | 24   transitionTable["G","G"] = NA | 
|  | 25   transitionTable["T","T"] = NA | 
|  | 26   write.table(x=transitionTable, file="transitions.txt", sep=",",quote=F,row.names=T,col.names=NA) | 
|  | 27   cat("0", file="n.txt") | 
|  | 28   stop("No data") | 
|  | 29 } | 
|  | 30 | 
|  | 31 | 
|  | 32 | 
|  | 33 cleanup_columns = c("FR1.IMGT.c.a", | 
|  | 34                     "FR2.IMGT.g.t", | 
|  | 35                     "CDR1.IMGT.Nb.of.nucleotides", | 
|  | 36                     "CDR2.IMGT.t.a", | 
|  | 37                     "FR1.IMGT.c.g", | 
|  | 38                     "CDR1.IMGT.c.t", | 
|  | 39                     "FR2.IMGT.a.c", | 
|  | 40                     "FR2.IMGT.Nb.of.mutations", | 
|  | 41                     "FR2.IMGT.g.c", | 
|  | 42                     "FR2.IMGT.a.g", | 
|  | 43                     "FR3.IMGT.t.a", | 
|  | 44                     "FR3.IMGT.t.c", | 
|  | 45                     "FR2.IMGT.g.a", | 
|  | 46                     "FR3.IMGT.c.g", | 
|  | 47                     "FR1.IMGT.Nb.of.mutations", | 
|  | 48                     "CDR1.IMGT.g.a", | 
|  | 49                     "CDR1.IMGT.t.g", | 
|  | 50                     "CDR1.IMGT.g.c", | 
|  | 51                     "CDR2.IMGT.Nb.of.nucleotides", | 
|  | 52                     "FR2.IMGT.a.t", | 
|  | 53                     "CDR1.IMGT.Nb.of.mutations", | 
|  | 54                     "CDR1.IMGT.a.g", | 
|  | 55                     "FR3.IMGT.a.c", | 
|  | 56                     "FR1.IMGT.g.a", | 
|  | 57                     "FR3.IMGT.a.g", | 
|  | 58                     "FR1.IMGT.a.t", | 
|  | 59                     "CDR2.IMGT.a.g", | 
|  | 60                     "CDR2.IMGT.Nb.of.mutations", | 
|  | 61                     "CDR2.IMGT.g.t", | 
|  | 62                     "CDR2.IMGT.a.c", | 
|  | 63                     "CDR1.IMGT.t.c", | 
|  | 64                     "FR3.IMGT.g.c", | 
|  | 65                     "FR1.IMGT.g.t", | 
|  | 66                     "FR3.IMGT.g.t", | 
|  | 67                     "CDR1.IMGT.a.t", | 
|  | 68                     "FR1.IMGT.a.g", | 
|  | 69                     "FR3.IMGT.a.t", | 
|  | 70                     "FR3.IMGT.Nb.of.nucleotides", | 
|  | 71                     "FR2.IMGT.t.c", | 
|  | 72                     "CDR2.IMGT.g.a", | 
|  | 73                     "FR2.IMGT.t.a", | 
|  | 74                     "CDR1.IMGT.t.a", | 
|  | 75                     "FR2.IMGT.t.g", | 
|  | 76                     "FR3.IMGT.t.g", | 
|  | 77                     "FR2.IMGT.Nb.of.nucleotides", | 
|  | 78                     "FR1.IMGT.t.a", | 
|  | 79                     "FR1.IMGT.t.g", | 
|  | 80                     "FR3.IMGT.c.t", | 
|  | 81                     "FR1.IMGT.t.c", | 
|  | 82                     "CDR2.IMGT.a.t", | 
|  | 83                     "FR2.IMGT.c.t", | 
|  | 84                     "CDR1.IMGT.g.t", | 
|  | 85                     "CDR2.IMGT.t.g", | 
|  | 86                     "FR1.IMGT.Nb.of.nucleotides", | 
|  | 87                     "CDR1.IMGT.c.g", | 
|  | 88                     "CDR2.IMGT.t.c", | 
|  | 89                     "FR3.IMGT.g.a", | 
|  | 90                     "CDR1.IMGT.a.c", | 
|  | 91                     "FR2.IMGT.c.a", | 
|  | 92                     "FR3.IMGT.Nb.of.mutations", | 
|  | 93                     "FR2.IMGT.c.g", | 
|  | 94                     "CDR2.IMGT.g.c", | 
|  | 95                     "FR1.IMGT.g.c", | 
|  | 96                     "CDR2.IMGT.c.t", | 
|  | 97                     "FR3.IMGT.c.a", | 
|  | 98                     "CDR1.IMGT.c.a", | 
|  | 99                     "CDR2.IMGT.c.g", | 
|  | 100                     "CDR2.IMGT.c.a", | 
|  | 101                     "FR1.IMGT.c.t", | 
|  | 102                     "FR1.IMGT.Nb.of.silent.mutations", | 
|  | 103                     "FR2.IMGT.Nb.of.silent.mutations", | 
|  | 104                     "FR3.IMGT.Nb.of.silent.mutations", | 
|  | 105                     "FR1.IMGT.Nb.of.nonsilent.mutations", | 
|  | 106                     "FR2.IMGT.Nb.of.nonsilent.mutations", | 
|  | 107                     "FR3.IMGT.Nb.of.nonsilent.mutations") | 
|  | 108 | 
|  | 109 for(col in cleanup_columns){ | 
|  | 110   dat[,col] = gsub("\\(.*\\)", "", dat[,col]) | 
|  | 111   #dat[dat[,col] == "",] = "0" | 
|  | 112   dat[,col] = as.numeric(dat[,col]) | 
|  | 113   dat[is.na(dat[,col]),] = 0 | 
|  | 114 } | 
|  | 115 | 
|  | 116 regions = c("FR1", "CDR1", "FR2", "CDR2", "FR3") | 
|  | 117 if(!include_fr1){ | 
|  | 118 	regions = c("CDR1", "FR2", "CDR2", "FR3") | 
|  | 119 } | 
|  | 120 | 
|  | 121 sum_by_row = function(x, columns) { sum(as.numeric(x[columns]), na.rm=T) } | 
|  | 122 | 
|  | 123 VRegionMutations_columns = paste(regions, ".IMGT.Nb.of.mutations", sep="") | 
|  | 124 dat$VRegionMutations =  apply(dat, FUN=sum_by_row, 1, columns=VRegionMutations_columns) | 
|  | 125 | 
|  | 126 VRegionNucleotides_columns = paste(regions, ".IMGT.Nb.of.nucleotides", sep="") | 
|  | 127 dat$VRegionNucleotides =  apply(dat, FUN=sum_by_row, 1, columns=VRegionNucleotides_columns) | 
|  | 128 | 
|  | 129 transitionMutations_columns = paste(rep(regions, each=4), c(".IMGT.a.g", ".IMGT.g.a", ".IMGT.c.t", ".IMGT.t.c"), sep="") | 
|  | 130 dat$transitionMutations = apply(dat, FUN=sum_by_row, 1, columns=transitionMutations_columns) | 
|  | 131 | 
|  | 132 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="") | 
|  | 133 dat$transversionMutations = apply(dat, FUN=sum_by_row, 1, columns=transversionMutations_columns) | 
|  | 134 | 
|  | 135 | 
|  | 136 transitionMutationsAtGC_columns = paste(rep(regions, each=2), c(".IMGT.g.a",".IMGT.c.t"), sep="") | 
|  | 137 dat$transitionMutationsAtGC = apply(dat, FUN=sum_by_row, 1, columns=transitionMutationsAtGC_columns) | 
|  | 138 | 
|  | 139 | 
|  | 140 totalMutationsAtGC_columns = paste(rep(regions, each=6), c(".IMGT.c.g",".IMGT.c.t",".IMGT.c.a",".IMGT.g.c",".IMGT.g.a",".IMGT.g.t"), sep="") | 
|  | 141 #totalMutationsAtGC_columns = paste(rep(regions, each=6), c(".IMGT.g.a",".IMGT.c.t",".IMGT.c.a",".IMGT.c.g",".IMGT.g.t"), sep="") | 
|  | 142 dat$totalMutationsAtGC = apply(dat, FUN=sum_by_row, 1, columns=totalMutationsAtGC_columns) | 
|  | 143 | 
|  | 144 transitionMutationsAtAT_columns = paste(rep(regions, each=2), c(".IMGT.a.g",".IMGT.t.c"), sep="") | 
|  | 145 dat$transitionMutationsAtAT = apply(dat, FUN=sum_by_row, 1, columns=transitionMutationsAtAT_columns) | 
|  | 146 | 
|  | 147 totalMutationsAtAT_columns = paste(rep(regions, each=6), c(".IMGT.a.g",".IMGT.a.c",".IMGT.a.t",".IMGT.t.g",".IMGT.t.c",".IMGT.t.a"), sep="") | 
|  | 148 #totalMutationsAtAT_columns = paste(rep(regions, each=5), c(".IMGT.a.g",".IMGT.t.c",".IMGT.a.c",".IMGT.g.c",".IMGT.t.g"), sep="") | 
|  | 149 dat$totalMutationsAtAT = apply(dat, FUN=sum_by_row, 1, columns=totalMutationsAtAT_columns) | 
|  | 150 | 
|  | 151 | 
|  | 152 FRRegions = regions[grepl("FR", regions)] | 
|  | 153 CDRRegions = regions[grepl("CDR", regions)] | 
|  | 154 | 
|  | 155 FR_silentMutations_columns = paste(FRRegions, ".IMGT.Nb.of.silent.mutations", sep="") | 
|  | 156 dat$silentMutationsFR = apply(dat, FUN=sum_by_row, 1, columns=FR_silentMutations_columns) | 
|  | 157 | 
|  | 158 CDR_silentMutations_columns = paste(CDRRegions, ".IMGT.Nb.of.silent.mutations", sep="") | 
|  | 159 dat$silentMutationsCDR = apply(dat, FUN=sum_by_row, 1, columns=CDR_silentMutations_columns) | 
|  | 160 | 
|  | 161 FR_nonSilentMutations_columns = paste(FRRegions, ".IMGT.Nb.of.nonsilent.mutations", sep="") | 
|  | 162 dat$nonSilentMutationsFR = apply(dat, FUN=sum_by_row, 1, columns=FR_nonSilentMutations_columns) | 
|  | 163 | 
|  | 164 CDR_nonSilentMutations_columns = paste(CDRRegions, ".IMGT.Nb.of.nonsilent.mutations", sep="") | 
|  | 165 dat$nonSilentMutationsCDR = apply(dat, FUN=sum_by_row, 1, columns=CDR_nonSilentMutations_columns) | 
|  | 166 | 
|  | 167 mutation.sum.columns = c("Sequence.ID", "VRegionMutations", "VRegionNucleotides", "transitionMutations", "transversionMutations", "transitionMutationsAtGC", "transitionMutationsAtAT", "silentMutationsFR", "nonSilentMutationsFR", "silentMutationsCDR", "nonSilentMutationsCDR") | 
|  | 168 | 
|  | 169 write.table(dat[,mutation.sum.columns], "mutation_by_id.txt", sep="\t",quote=F,row.names=F,col.names=T) | 
|  | 170 | 
|  | 171 setwd(outputdir) | 
|  | 172 | 
|  | 173 nts = c("a", "c", "g", "t") | 
|  | 174 zeros=rep(0, 4) | 
|  | 175 matrx = matrix(data = 0, ncol=((length(genes) + 1) * 3),nrow=9) | 
|  | 176 for(i in 1:length(genes)){ | 
|  | 177   gene = genes[i] | 
|  | 178   tmp = dat[grepl(paste(".*", gene, ".*", sep=""), dat$best_match),] | 
|  | 179   if(gene == "."){ | 
|  | 180     tmp = dat | 
|  | 181   } | 
|  | 182   j = i - 1 | 
|  | 183   x = (j * 3) + 1 | 
|  | 184   y = (j * 3) + 2 | 
|  | 185   z = (j * 3) + 3 | 
|  | 186   matrx[1,x] = sum(tmp$VRegionMutations) | 
|  | 187   matrx[1,y] = sum(tmp$VRegionNucleotides) | 
|  | 188   matrx[1,z] = round(matrx[1,x] / matrx[1,y] * 100, digits=1) | 
|  | 189 | 
|  | 190   matrx[2,x] = sum(tmp$transitionMutations) | 
|  | 191   matrx[2,y] = sum(tmp$VRegionMutations) | 
|  | 192   matrx[2,z] = round(matrx[2,x] / matrx[2,y] * 100, digits=1) | 
|  | 193 | 
|  | 194   matrx[3,x] = sum(tmp$transversionMutations) | 
|  | 195   matrx[3,y] = sum(tmp$VRegionMutations) | 
|  | 196   matrx[3,z] = round(matrx[3,x] / matrx[3,y] * 100, digits=1) | 
|  | 197 | 
|  | 198   matrx[4,x] = sum(tmp$transitionMutationsAtGC) | 
|  | 199   matrx[4,y] = sum(tmp$totalMutationsAtGC) | 
|  | 200   matrx[4,z] = round(matrx[4,x] / matrx[4,y] * 100, digits=1) | 
|  | 201 | 
|  | 202   matrx[5,x] = sum(tmp$totalMutationsAtGC) | 
|  | 203   matrx[5,y] = sum(tmp$VRegionMutations) | 
|  | 204   matrx[5,z] = round(matrx[5,x] / matrx[5,y] * 100, digits=1) | 
|  | 205 | 
|  | 206   matrx[6,x] = sum(tmp$transitionMutationsAtAT) | 
|  | 207   matrx[6,y] = sum(tmp$totalMutationsAtAT) | 
|  | 208   matrx[6,z] = round(matrx[6,x] / matrx[6,y] * 100, digits=1) | 
|  | 209 | 
|  | 210   matrx[7,x] = sum(tmp$totalMutationsAtAT) | 
|  | 211   matrx[7,y] = sum(tmp$VRegionMutations) | 
|  | 212   matrx[7,z] = round(matrx[7,x] / matrx[7,y] * 100, digits=1) | 
|  | 213 | 
|  | 214   matrx[8,x] = sum(tmp$nonSilentMutationsFR) | 
|  | 215   matrx[8,y] = sum(tmp$silentMutationsFR) | 
|  | 216   matrx[8,z] = round(matrx[8,x] / matrx[8,y], digits=1) | 
|  | 217 | 
|  | 218   matrx[9,x] = sum(tmp$nonSilentMutationsCDR) | 
|  | 219   matrx[9,y] = sum(tmp$silentMutationsCDR) | 
|  | 220   matrx[9,z] = round(matrx[9,x] / matrx[9,y], digits=1) | 
|  | 221 | 
|  | 222 | 
|  | 223   transitionTable = data.frame(A=zeros,C=zeros,G=zeros,T=zeros) | 
|  | 224   row.names(transitionTable) = c("A", "C", "G", "T") | 
|  | 225   transitionTable["A","A"] = NA | 
|  | 226   transitionTable["C","C"] = NA | 
|  | 227   transitionTable["G","G"] = NA | 
|  | 228   transitionTable["T","T"] = NA | 
|  | 229 | 
|  | 230   if(nrow(tmp) > 0){ | 
|  | 231 		for(nt1 in nts){ | 
|  | 232 			for(nt2 in nts){ | 
|  | 233 				if(nt1 == nt2){ | 
|  | 234 					next | 
|  | 235 				} | 
|  | 236 				NT1 = LETTERS[letters == nt1] | 
|  | 237 				NT2 = LETTERS[letters == nt2] | 
|  | 238 				FR1 = paste("FR1.IMGT.", nt1, ".", nt2, sep="") | 
|  | 239 				CDR1 = paste("CDR1.IMGT.", nt1, ".", nt2, sep="") | 
|  | 240 				FR2 = paste("FR2.IMGT.", nt1, ".", nt2, sep="") | 
|  | 241 				CDR2 = paste("CDR2.IMGT.", nt1, ".", nt2, sep="") | 
|  | 242 				FR3 = paste("FR3.IMGT.", nt1, ".", nt2, sep="") | 
|  | 243 				if(include_fr1){ | 
|  | 244 					transitionTable[NT1,NT2] = sum(tmp[,c(FR1, CDR1, FR2, CDR2, FR3)]) | 
|  | 245 				} else { | 
|  | 246 					transitionTable[NT1,NT2] = sum(tmp[,c(CDR1, FR2, CDR2, FR3)]) | 
|  | 247 				} | 
|  | 248 			} | 
|  | 249 		} | 
|  | 250   } | 
|  | 251 | 
|  | 252 | 
|  | 253   write.table(x=transitionTable, file=paste("transitions_", gene ,".txt", sep=""), sep=",",quote=F,row.names=T,col.names=NA) | 
|  | 254   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) | 
|  | 255 | 
|  | 256   cat(matrx[1,x], file=paste(gene, "_value.txt" ,sep="")) | 
|  | 257   cat(length(tmp$Sequence.ID), file=paste(gene, "_n.txt" ,sep="")) | 
|  | 258 } | 
|  | 259 | 
|  | 260 #again for all of the data | 
|  | 261 tmp = dat | 
|  | 262 j = i | 
|  | 263 x = (j * 3) + 1 | 
|  | 264 y = (j * 3) + 2 | 
|  | 265 z = (j * 3) + 3 | 
|  | 266 matrx[1,x] = sum(tmp$VRegionMutations) | 
|  | 267 matrx[1,y] = sum(tmp$VRegionNucleotides) | 
|  | 268 matrx[1,z] = round(matrx[1,x] / matrx[1,y] * 100, digits=1) | 
|  | 269 | 
|  | 270 matrx[2,x] = sum(tmp$transitionMutations) | 
|  | 271 matrx[2,y] = sum(tmp$VRegionMutations) | 
|  | 272 matrx[2,z] = round(matrx[2,x] / matrx[2,y] * 100, digits=1) | 
|  | 273 | 
|  | 274 matrx[3,x] = sum(tmp$transversionMutations) | 
|  | 275 matrx[3,y] = sum(tmp$VRegionMutations) | 
|  | 276 matrx[3,z] = round(matrx[3,x] / matrx[3,y] * 100, digits=1) | 
|  | 277 | 
|  | 278 matrx[4,x] = sum(tmp$transitionMutationsAtGC) | 
|  | 279 matrx[4,y] = sum(tmp$totalMutationsAtGC) | 
|  | 280 matrx[4,z] = round(matrx[4,x] / matrx[4,y] * 100, digits=1) | 
|  | 281 | 
|  | 282 matrx[5,x] = sum(tmp$totalMutationsAtGC) | 
|  | 283 matrx[5,y] = sum(tmp$VRegionMutations) | 
|  | 284 matrx[5,z] = round(matrx[5,x] / matrx[5,y] * 100, digits=1) | 
|  | 285 | 
|  | 286 matrx[6,x] = sum(tmp$transitionMutationsAtAT) | 
|  | 287 matrx[6,y] = sum(tmp$totalMutationsAtAT) | 
|  | 288 matrx[6,z] = round(matrx[6,x] / matrx[6,y] * 100, digits=1) | 
|  | 289 | 
|  | 290 matrx[7,x] = sum(tmp$totalMutationsAtAT) | 
|  | 291 matrx[7,y] = sum(tmp$VRegionMutations) | 
|  | 292 matrx[7,z] = round(matrx[7,x] / matrx[7,y] * 100, digits=1) | 
|  | 293 | 
|  | 294 matrx[8,x] = sum(tmp$nonSilentMutationsFR) | 
|  | 295 matrx[8,y] = sum(tmp$silentMutationsFR) | 
|  | 296 matrx[8,z] = round(matrx[8,x] / matrx[8,y], digits=1) | 
|  | 297 | 
|  | 298 matrx[9,x] = sum(tmp$nonSilentMutationsCDR) | 
|  | 299 matrx[9,y] = sum(tmp$silentMutationsCDR) | 
|  | 300 matrx[9,z] = round(matrx[9,x] / matrx[9,y], digits=1) | 
|  | 301 | 
|  | 302 transitionTable = data.frame(A=1:4,C=1:4,G=1:4,T=1:4) | 
|  | 303 row.names(transitionTable) = c("A", "C", "G", "T") | 
|  | 304 transitionTable["A","A"] = NA | 
|  | 305 transitionTable["C","C"] = NA | 
|  | 306 transitionTable["G","G"] = NA | 
|  | 307 transitionTable["T","T"] = NA | 
|  | 308 | 
|  | 309 | 
|  | 310 for(nt1 in nts){ | 
|  | 311 	for(nt2 in nts){ | 
|  | 312 		if(nt1 == nt2){ | 
|  | 313 			next | 
|  | 314 		} | 
|  | 315 		NT1 = LETTERS[letters == nt1] | 
|  | 316 		NT2 = LETTERS[letters == nt2] | 
|  | 317 		FR1 = paste("FR1.IMGT.", nt1, ".", nt2, sep="") | 
|  | 318 		CDR1 = paste("CDR1.IMGT.", nt1, ".", nt2, sep="") | 
|  | 319 		FR2 = paste("FR2.IMGT.", nt1, ".", nt2, sep="") | 
|  | 320 		CDR2 = paste("CDR2.IMGT.", nt1, ".", nt2, sep="") | 
|  | 321 		FR3 = paste("FR3.IMGT.", nt1, ".", nt2, sep="") | 
|  | 322 		if(include_fr1){ | 
|  | 323 			transitionTable[NT1,NT2] = sum(tmp[,c(FR1, CDR1, FR2, CDR2, FR3)]) | 
|  | 324 		} else { | 
|  | 325 			transitionTable[NT1,NT2] = sum(tmp[,c(CDR1, FR2, CDR2, FR3)]) | 
|  | 326 		} | 
|  | 327 	} | 
|  | 328 } | 
|  | 329 write.table(x=transitionTable, file="transitions.txt", sep=",",quote=F,row.names=T,col.names=NA) | 
|  | 330 write.table(x=tmp[,c("Sequence.ID", "best_match", "chunk_hit_percentage", "nt_hit_percentage", "start_locations")], file="matched_all.txt", sep="\t",quote=F,row.names=F,col.names=T) | 
|  | 331 cat(matrx[1,x], file="total_value.txt") | 
|  | 332 cat(length(tmp$Sequence.ID), file="total_n.txt") | 
|  | 333 | 
|  | 334 | 
|  | 335 | 
|  | 336 result = data.frame(matrx) | 
|  | 337 row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C G (%)", "Transitions at A T (%)", "Targeting of A T (%)", "FR R/S (ratio)", "CDR R/S (ratio)") | 
|  | 338 | 
|  | 339 write.table(x=result, file="mutations.txt", sep=",",quote=F,row.names=T,col.names=F) | 
|  | 340 | 
|  | 341 | 
|  | 342 if (!("ggplot2" %in% rownames(installed.packages()))) { | 
|  | 343 	install.packages("ggplot2", repos="http://cran.xl-mirror.nl/") | 
|  | 344 } | 
|  | 345 | 
|  | 346 | 
|  | 347 genesForPlot = gsub("[0-9]", "", dat$best_match) | 
|  | 348 genesForPlot = data.frame(table(genesForPlot)) | 
|  | 349 colnames(genesForPlot) = c("Gene","Freq") | 
|  | 350 genesForPlot$label = paste(genesForPlot$Gene, "-", genesForPlot$Freq) | 
|  | 351 write.table(genesForPlot, "all.txt", sep="\t",quote=F,row.names=F,col.names=T) | 
|  | 352 | 
|  | 353 | 
|  | 354 pc = ggplot(genesForPlot, aes(x = factor(1), y=Freq, fill=label)) | 
|  | 355 pc = pc + geom_bar(width = 1, stat = "identity") | 
|  | 356 pc = pc + coord_polar(theta="y") | 
|  | 357 pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("Classes", "( n =", sum(genesForPlot$Freq), ")")) | 
|  | 358 | 
|  | 359 png(filename="all.png") | 
|  | 360 pc | 
|  | 361 dev.off() | 
|  | 362 | 
|  | 363 | 
|  | 364 #blegh | 
|  | 365 genesForPlot = dat[grepl("ca", dat$best_match),]$best_match | 
|  | 366 if(length(genesForPlot) > 0){ | 
|  | 367 	genesForPlot = data.frame(table(genesForPlot)) | 
|  | 368 	colnames(genesForPlot) = c("Gene","Freq") | 
|  | 369 	genesForPlot$label = paste(genesForPlot$Gene, "-", genesForPlot$Freq) | 
|  | 370 | 
|  | 371 	pc = ggplot(genesForPlot, aes(x = factor(1), y=Freq, fill=label)) | 
|  | 372 	pc = pc + geom_bar(width = 1, stat = "identity") | 
|  | 373 	pc = pc + coord_polar(theta="y") | 
|  | 374 	pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("IgA subclasses", "( n =", sum(genesForPlot$Freq), ")")) | 
|  | 375 	write.table(genesForPlot, "ca.txt", sep="\t",quote=F,row.names=F,col.names=T) | 
|  | 376 | 
|  | 377 	png(filename="ca.png") | 
|  | 378 	print(pc) | 
|  | 379 	dev.off() | 
|  | 380 } | 
|  | 381 | 
|  | 382 genesForPlot = dat[grepl("cg", dat$best_match),]$best_match | 
|  | 383 if(length(genesForPlot) > 0){ | 
|  | 384 	genesForPlot = data.frame(table(genesForPlot)) | 
|  | 385 	colnames(genesForPlot) = c("Gene","Freq") | 
|  | 386 	genesForPlot$label = paste(genesForPlot$Gene, "-", genesForPlot$Freq) | 
|  | 387 | 
|  | 388 	pc = ggplot(genesForPlot, aes(x = factor(1), y=Freq, fill=label)) | 
|  | 389 	pc = pc + geom_bar(width = 1, stat = "identity") | 
|  | 390 	pc = pc + coord_polar(theta="y") | 
|  | 391 	pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("IgG subclasses", "( n =", sum(genesForPlot$Freq), ")")) | 
|  | 392 	write.table(genesForPlot, "cg.txt", sep="\t",quote=F,row.names=F,col.names=T) | 
|  | 393 | 
|  | 394 	png(filename="cg.png") | 
|  | 395 	print(pc) | 
|  | 396 	dev.off() | 
|  | 397 } | 
|  | 398 | 
|  | 399 dat$percentage_mutations = round(dat$VRegionMutations / dat$VRegionNucleotides * 100, 2) | 
|  | 400 | 
|  | 401 p = ggplot(dat, aes(best_match, percentage_mutations)) | 
|  | 402 p = p + geom_point(aes(colour=best_match), position="jitter") + geom_boxplot(aes(middle=mean(percentage_mutations)), alpha=0.1, outlier.shape = NA) | 
|  | 403 p = p + xlab("Subclass") + ylab("Frequency") + ggtitle("Frequency scatter plot") | 
|  | 404 | 
|  | 405 png(filename="scatter.png") | 
|  | 406 print(p) | 
|  | 407 dev.off() | 
|  | 408 | 
|  | 409 write.table(dat[,c("Sequence.ID", "best_match", "VRegionMutations", "VRegionNucleotides", "percentage_mutations")], "scatter.txt", sep="\t",quote=F,row.names=F,col.names=T) | 
|  | 410 | 
|  | 411 write.table(dat, input, sep="\t",quote=F,row.names=F,col.names=T) | 
|  | 412 | 
|  | 413 | 
|  | 414 | 
|  | 415 | 
|  | 416 | 
|  | 417 | 
|  | 418 dat$best_match_class = substr(dat$best_match, 0, 2) | 
|  | 419 freq_labels = c("0", "0-2", "2-5", "5-10", "10-15", "15-20", "20") | 
|  | 420 dat$frequency_bins = cut(dat$percentage_mutations, breaks=c(-Inf, 0, 2,5,10,15,20, Inf), labels=freq_labels) | 
|  | 421 | 
|  | 422 frequency_bins_data = data.frame(data.table(dat)[, list(frequency_count=.N), by=c("best_match_class", "frequency_bins")]) | 
|  | 423 | 
|  | 424 p = ggplot(frequency_bins_data, aes(frequency_bins, frequency_count)) | 
|  | 425 p = p + geom_bar(aes(fill=best_match_class), stat="identity", position="dodge") | 
|  | 426 p = p + xlab("Frequency ranges") + ylab("Frequency") + ggtitle("Mutation Frequencies by class") | 
|  | 427 | 
|  | 428 png(filename="frequency_ranges.png") | 
|  | 429 print(p) | 
|  | 430 dev.off() | 
|  | 431 | 
|  | 432 frequency_bins_data_by_class = frequency_bins_data | 
|  | 433 | 
|  | 434 write.table(frequency_bins_data_by_class, "frequency_ranges_classes.txt", sep="\t",quote=F,row.names=F,col.names=T) | 
|  | 435 | 
|  | 436 frequency_bins_data = data.frame(data.table(dat)[, list(frequency_count=.N), by=c("best_match", "frequency_bins")]) | 
|  | 437 | 
|  | 438 write.table(frequency_bins_data, "frequency_ranges_subclasses.txt", sep="\t",quote=F,row.names=F,col.names=T) | 
|  | 439 | 
|  | 440 | 
|  | 441 #frequency_bins_data_by_class | 
|  | 442 #frequency_ranges_subclasses.txt | 
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