Mercurial > repos > davidvanzessen > shm_csr

comparison sequence_overview.r @ 39:a24f8c93583a draft

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Uploaded
author davidvanzessen
date Thu, 22 Dec 2016 09:39:27 -0500
parents 22fabe161cf3
children b66e8946ba75
comparison
equal deleted inserted replaced
38:05c62efdc393 39:a24f8c93583a
68 res = paste(res, tr(df[i,]), sep="") 68 res = paste(res, tr(df[i,]), sep="")
69 } 69 }
70 res = paste(res, "</table>") 70 res = paste(res, "</table>")
71 } 71 }
72 72
73 cat("<table border='1' class='pure-table pure-table-striped'>", file=main.html, append=F) 73 cat("<center><img src='data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAA8AAAAPCAYAAAA71pVKAAAAzElEQVQoka2TwQ2CQBBFpwTshw4ImW8ogJMlUIMmhNCDxgasAi50oSXA8XlAjCG7aqKTzGX/vsnM31mzR0gk7tTudO5MEizpzvQ4ryUSe408J3Xn+grE0p1rnpOamVmWsZG4rS+dzzAMsN8Hi9yyjI1JNGtxu4VxBJgLRLpoTKIPiW0LlwtUVRTubW2OBGUJu92cZRmdfbKQMAw8o+vi5v0fLorZ7Y9waGYJjsf38DJz0O1PsEQffOcv4Sa6YYfDDJ5Obzbsp93+5VfdATueO1fdLdI0AAAAAElFTkSuQmCC'> Please note that this tab is based on all sequences before filter unique sequences and the remove duplicates based on filters are applied. In this table only sequences according more than once are included. </center>", file=main.html, append=F)
74 cat("<table border='1' class='pure-table pure-table-striped'>", file=main.html, append=T)
74 75
75 if(empty.region.filter == "leader"){ 76 if(empty.region.filter == "leader"){
76 cat("<caption>FR1+CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T) 77 cat("<caption>FR1+CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T)
77 } else if(empty.region.filter == "FR1"){ 78 } else if(empty.region.filter == "FR1"){
78 cat("<caption>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T) 79 cat("<caption>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T)
303 tmp = names(NTresult) 304 tmp = names(NTresult)
304 NTresult = cbind(NTresult, data.frame(new.col.x, new.col.y, new.col.z)) 305 NTresult = cbind(NTresult, data.frame(new.col.x, new.col.y, new.col.z))
305 names(NTresult) = c(tmp, paste(clazz, c("x", "y", "z"), sep="")) 306 names(NTresult) = c(tmp, paste(clazz, c("x", "y", "z"), sep=""))
306 } 307 }
307 308
308 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) 309 NToverview.tmp = NToverview[,c("Sequence.ID", "best_match", "seq", "A", "C", "G", "T")]
310
311 names(NToverview.tmp) = c("Sequence.ID", "best_match", "Sequence of the analysed region", "A", "C", "G", "T")
312
313 write.table(NToverview.tmp, NToverview.file, quote=F, sep="\t", row.names=F, col.names=T)
309 314
310 NToverview = NToverview[!grepl("unmatched", NToverview$best_match),] 315 NToverview = NToverview[!grepl("unmatched", NToverview$best_match),]
311 316
312 new.col.x = c(sum(NToverview$A), sum(NToverview$C), sum(NToverview$T), sum(NToverview$G)) 317 new.col.x = c(sum(NToverview$A), sum(NToverview$C), sum(NToverview$T), sum(NToverview$G))
313 new.col.y = sum(new.col.x) 318 new.col.y = sum(new.col.x)