Commit 4b00e22457ceceba11ea1832884a9d7de7e69361
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AverageNetwork3.R
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1 | +#source("/home/zgong001/Documents/Alarm/D50C9v/RCode/CombineOrders.R") | |
2 | +getRelation = | |
3 | + function(st = "[6][8][5][7|6:8:5][1|7][3|7:1][4|1][2|4][0|2]"){ | |
4 | + re = c() | |
5 | + temstr = substr(st, 2, nchar(st)-1) | |
6 | + stlist = strsplit(chartr(old = "][", new = "##", temstr), "##") | |
7 | + for(i in 1:length(stlist[[1]])){ | |
8 | + temc = chartr(old = "|", new = "g", stlist[[1]][i]) | |
9 | + | |
10 | + if (grepl("g", temc)){ | |
11 | + temc2 = strsplit(temc, "g") | |
12 | + | |
13 | + X = temc2[[1]][1] | |
14 | + TY = strsplit(temc2[[1]][2], ":") | |
15 | + for(j in 1:length(TY[[1]])){ | |
16 | + Y = TY[[1]][j] | |
17 | + | |
18 | + cc= paste(Y,"->", X, sep = "") | |
19 | + re = append(re, cc) | |
20 | + } | |
21 | + } | |
22 | + } | |
23 | + return(re) | |
24 | + } | |
25 | + | |
26 | +creatDataframe = | |
27 | + function(v = c("0", "1","2","3","4","5","6","7","8"), r = 246){ | |
28 | + cn = c() | |
29 | + co= combn(v,2) | |
30 | + for(i in 1:ncol(co)){ | |
31 | + X = co[1,i] | |
32 | + Y = co[2,i] | |
33 | + c1 = paste(X, "->", Y, sep = "") | |
34 | + cn = append(cn,c1) | |
35 | + c2 = paste(Y, "->", X, sep = "") | |
36 | + cn = append(cn,c2) | |
37 | + c3 = paste(X, " NA ", Y, sep = "") | |
38 | + cn = append(cn,c3) | |
39 | + } | |
40 | + | |
41 | + b= ncol(co) | |
42 | + | |
43 | + re = data.frame(matrix(0, nrow=r, ncol=b*3)) | |
44 | + colnames(re) = cn | |
45 | + | |
46 | + return(re) | |
47 | + } | |
48 | + | |
49 | +#--------------------------------------------------------------------------------- | |
50 | +sortStru = function(st = "[5][6][8][7|5:8][1|5:7][3|7:8][2|6:1][4|1][0|2]"){ | |
51 | + library(dplyr) | |
52 | + re = "" | |
53 | + temstr = substr(st, 2, nchar(st)-1) | |
54 | + stlist = strsplit(chartr(old = "][", new = "##", temstr), "##") | |
55 | + stlist = sort(stlist[[1]]) | |
56 | + for(i in 1:length(stlist)){ | |
57 | + if(nchar(stlist[i])>3){ | |
58 | + | |
59 | + temc = chartr(old = "|", new = "g", stlist[i]) | |
60 | + | |
61 | + temc2 = strsplit(temc, "g") | |
62 | + X = temc2[[1]][1] | |
63 | + TY = strsplit(temc2[[1]][2], ":") | |
64 | + TY = sort(TY[[1]]) | |
65 | + | |
66 | + TY2 = paste(TY, collapse = ":") | |
67 | + | |
68 | + stlist[i] = paste(X,"|", TY2, sep = "") | |
69 | + | |
70 | + stlist[i] <- TY %>% | |
71 | + paste(., collapse=":") %>% | |
72 | + paste(X, "|", ., sep = "") | |
73 | + | |
74 | + } | |
75 | + | |
76 | + } | |
77 | + | |
78 | + re <- stlist %>% | |
79 | + paste(., collapse="][") %>% | |
80 | + paste("[", ., "]", sep = "") | |
81 | + | |
82 | + return(re) | |
83 | +} | |
84 | + | |
85 | +MB = | |
86 | + function (struc ="[6][8][5][7|6:8:5][3|7][1|7:3][4|1][2|4][0|2]", v ="1"){ | |
87 | + | |
88 | + library(xlsx) | |
89 | + library(bnlearn) | |
90 | + library(dplyr) | |
91 | + | |
92 | + | |
93 | + mbs = "" | |
94 | + | |
95 | + strutem <- struc %>% | |
96 | + as.character(.) %>% | |
97 | + substr(., 2, nchar(.)-1) | |
98 | + | |
99 | + stru = strsplit(chartr(old = "][", new = "##", strutem), "##") | |
100 | + | |
101 | + for(j in 1:length(stru[[1]])){ | |
102 | + if(grepl(v,stru[[1]][j])){ | |
103 | + mbs = paste(mbs, "[", stru[[1]][j], "]", sep = "") | |
104 | + } | |
105 | + } | |
106 | + return(mbs) | |
107 | + } | |
108 | + | |
109 | +sumTable = | |
110 | + function (pathname = "/home/zgong001/Documents/Alarm/D1KC9v/D1KC9v BestOrders/Strus_D1KC9v.txt", | |
111 | + t = c("B-W", "AIFM1", "ATP6V1C2", "CACNA1D", "CACNB1", "CDH15", "CLDN6", "DDIT3", "EIF2AK3", "ENDOG", "HRK", | |
112 | + "LMNB1" ,"MAPK12", "NRF1", "PARP1" ,"PCK2", "PLA2G4C", "PPP2R3B", "VDAC2", "VDAC3"), | |
113 | + exfilename = "/home/zgong001/Documents/Alarm/D1KC9v/D1KC9v BestOrders/Strus_D1KC9v.xlsx"){ | |
114 | + library(bnlearn) | |
115 | + library(xlsx) | |
116 | + library(dplyr) | |
117 | + | |
118 | + v = as.character(seq(0,length(t)-1),1) | |
119 | + suminput = read.table(pathname, header = FALSE) | |
120 | + suminput = na.omit(suminput) | |
121 | + sumResu = data.frame() | |
122 | + n = ncol(suminput) | |
123 | + ord = vector() | |
124 | + | |
125 | + for(l in 1:nrow(suminput)){ | |
126 | + tem = suminput[l,1] | |
127 | + for(m in 2:(n-4)){ | |
128 | + tem = paste(tem, suminput[l,m], sep = " ") | |
129 | + } | |
130 | + ord = append(ord, tem) | |
131 | + } | |
132 | + | |
133 | + | |
134 | + suminput = cbind(suminput, ord) | |
135 | + | |
136 | + | |
137 | + suminput = suminput[-n] | |
138 | + | |
139 | + for(j in (n-4):1){ | |
140 | + suminput = suminput[,-j] | |
141 | + } | |
142 | + | |
143 | + colnames(suminput)[1] <- "OrderScores" | |
144 | + colnames(suminput)[2] <- "Structures" | |
145 | + colnames(suminput)[3] <- "StructScores" | |
146 | + | |
147 | + orders= aggregate( OrderScores ~ord, data=suminput, FUN = mean) | |
148 | + orders = orders[order(-orders[,2]), ] | |
149 | + for(i in 1:nrow(orders)){ | |
150 | + orders$Opercentage[i] = exp(-log(sum(exp(orders$OrderScores-orders$OrderScores[i])))) | |
151 | + } | |
152 | + | |
153 | + orders$Ocumper = cumsum(orders$Opercentage) | |
154 | + | |
155 | + for(i in 1:nrow(orders)){ | |
156 | + tem = suminput[which(suminput$ord== orders[i,1]), ] | |
157 | + | |
158 | + tem$Opercentage = orders[i,3] | |
159 | + tem$Ocumper = orders[i,4] | |
160 | + | |
161 | + for(j in 1:nrow(tem)){ | |
162 | + tem$Spercentage[j] = exp(-log(sum(exp(tem$StructScores-tem$StructScores[j])))) | |
163 | + } | |
164 | + tem$Scumper = cumsum(tem$Spercentage) | |
165 | + tem = tem[c("ord", "OrderScores", "Opercentage","Ocumper", "Structures", "StructScores","Spercentage","Scumper")] | |
166 | + sumResu = rbind(sumResu, tem) | |
167 | + } | |
168 | + | |
169 | + | |
170 | + for(k in 1:nrow(sumResu)){ | |
171 | + sumResu$sortS[k] = sortStru(as.character(sumResu$Structures[k])) | |
172 | + } | |
173 | + | |
174 | + rs = nrow(sumResu) | |
175 | + | |
176 | + rl = creatDataframe(v,rs) | |
177 | + sumResu= cbind(sumResu, rl) | |
178 | + | |
179 | + # sumAnce = sumResu | |
180 | + | |
181 | + co= combn(v,2) | |
182 | + | |
183 | + for(i in 1:nrow(sumResu)){ | |
184 | + s = as.character(sumResu [i,5]) | |
185 | + rel = getRelation(st = s) | |
186 | + | |
187 | + for(j in 1:ncol(co)){ | |
188 | + X = co[1,j] | |
189 | + Y = co[2,j] | |
190 | + c1 = paste(X, "->", Y, sep = "") | |
191 | + c2 = paste(Y, "->", X, sep = "") | |
192 | + c3 = paste(X, " NA ", Y, sep = "") | |
193 | + | |
194 | + if (c1 %in% rel){ | |
195 | + sumResu[i,c1] = sumResu$Opercentage[i]*sumResu$Spercentage[i] | |
196 | + } | |
197 | + else if(c2 %in% rel){ | |
198 | + sumResu[i,c2] = sumResu$Opercentage[i]*sumResu$Spercentage[i] | |
199 | + } | |
200 | + else{ | |
201 | + sumResu[i,c3] = sumResu$Opercentage[i]*sumResu$Spercentage[i] | |
202 | + } | |
203 | + | |
204 | + } | |
205 | + | |
206 | + } | |
207 | + | |
208 | + # print(sumResu) | |
209 | + | |
210 | + sumP = colSums(sumResu[, -c(1:9)]) | |
211 | + | |
212 | + # print (sumP) | |
213 | + | |
214 | + ########################################## | |
215 | + | |
216 | + | |
217 | + | |
218 | + StruWithO = aggregate( StructScores ~sortS, data=sumResu, FUN = mean) | |
219 | + | |
220 | + for(l in 1:nrow(StruWithO)){ | |
221 | + StruWithO$Spercentage[l] = exp(-log(sum(exp(StruWithO$StructScores-StruWithO$StructScores[l])))) | |
222 | + } | |
223 | + | |
224 | + StruWithO = StruWithO[order(-StruWithO[,3]), ] | |
225 | + | |
226 | + rss = nrow(StruWithO) | |
227 | + | |
228 | + rls = creatDataframe(v,rss) | |
229 | + StruWithO= cbind(StruWithO, rls) | |
230 | + | |
231 | + for(m in 1:nrow(StruWithO)){ | |
232 | + ss = as.character(StruWithO [m,1]) | |
233 | + rels = getRelation(st = ss) | |
234 | + # print(rels) | |
235 | + | |
236 | + for(n in 1:ncol(co)){ | |
237 | + X = co[1,n] | |
238 | + Y = co[2,n] | |
239 | + c1 = paste(X, "->", Y, sep = "") | |
240 | + c2 = paste(Y, "->", X, sep = "") | |
241 | + c3 = paste(X, " NA ", Y, sep = "") | |
242 | + | |
243 | + if (c1 %in% rels){ | |
244 | + StruWithO[m,c1] = StruWithO$Spercentage[m] | |
245 | + } | |
246 | + else if(c2 %in% rels){ | |
247 | + StruWithO[m,c2] = StruWithO$Spercentage[m] | |
248 | + } | |
249 | + else{ | |
250 | + StruWithO[m,c3] = StruWithO$Spercentage[m] | |
251 | + } | |
252 | + | |
253 | + } | |
254 | + | |
255 | + } | |
256 | + | |
257 | + | |
258 | + sumpS = colSums(StruWithO[, -c(1:3)]) | |
259 | + # print(sumpS) | |
260 | + | |
261 | + # totS = (sumP+sumpS)/2 | |
262 | + | |
263 | + # nam = names(totS) | |
264 | + nam = names(sumP) | |
265 | + | |
266 | + # nam2 = names(sumpS) | |
267 | + | |
268 | + # print(nam2) | |
269 | + | |
270 | + for(i in 1:length(nam)){ | |
271 | + if (grepl("->", nam[i])){ | |
272 | + TY = strsplit(nam[i], "->") | |
273 | + a = as.numeric(TY[[1]][1]) | |
274 | + b = as.numeric(TY[[1]][2]) | |
275 | + nam[i] = paste(t[a+1], "->", t[b+1], sep = "") | |
276 | + } | |
277 | + | |
278 | + if (grepl(" NA ", nam[i])){ | |
279 | + TY = strsplit(nam[i], " NA ") | |
280 | + a = as.numeric(TY[[1]][1]) | |
281 | + b = as.numeric(TY[[1]][2]) | |
282 | + nam[i] = paste(t[a+1], " NA ", t[b+1], sep = "") | |
283 | + } | |
284 | + | |
285 | + } | |
286 | + | |
287 | + # print(nam) | |
288 | + names(sumP) = nam | |
289 | + names(sumpS) = nam | |
290 | + | |
291 | + sumP = as.data.frame(sumP) | |
292 | + sumpS = as.data.frame(sumpS) | |
293 | + | |
294 | + # print(sumP) | |
295 | + | |
296 | + # print(totS) | |
297 | + | |
298 | + write.xlsx(sumP, exfilename, sheetName = "Pairs", col.names = TRUE, row.names = TRUE, append = FALSE) | |
299 | + write.xlsx(sumpS, exfilename, sheetName = "Pairs-WO", col.names = TRUE, row.names = TRUE, append = TRUE) | |
300 | + | |
301 | + # return(sumpS) | |
302 | + | |
303 | + } | |
304 | + | |
305 | + | |
306 | + | |
307 | +AverageNet = function(pathname = "/home/zgong001/Documents/Projects/Luminal/3/SS/Pairs-A3-Luminal A-A-B.xlsx", | |
308 | + outfile = "/home/zgong001/Documents/dot/out.gv"){ | |
309 | + | |
310 | + library(xlsx) | |
311 | + | |
312 | + res <- read.xlsx(pathname, 1) # read first sheet | |
313 | + res = na.omit(res) | |
314 | + | |
315 | + cat("digraph G {", file=outfile, sep="\n") | |
316 | + | |
317 | + p = round(nrow(res)/3) | |
318 | + | |
319 | + for(i in 1:p){ | |
320 | + | |
321 | + t = (i-1)*3 | |
322 | + v = as.vector(res[(t+1):(t+3),2]) | |
323 | + names(v) = res[(t+1):(t+3),1] | |
324 | + m = sort(v, decreasing = TRUE) | |
325 | + mn = names(m[1]) | |
326 | + if(grepl("->", mn)){ | |
327 | + if(grepl("->", names(m[2]))){ | |
328 | + cat("\t", mn, " [penwidth=", round(m[[1]]*2,digits = 2), ",", 'label="', round(m[[1]]*100 ,digits = 2), " (", round(m[[2]]*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE) | |
329 | + } | |
330 | + else{ | |
331 | + cat("\t", mn, " [penwidth=", round(m[[1]]*2,digits = 2), ",", 'label="', round(m[[1]]*100,digits = 2) , " (", round(m[[3]]*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE) | |
332 | + } | |
333 | + | |
334 | + } | |
335 | + | |
336 | + } | |
337 | + | |
338 | + cat("}", file=outfile, append=TRUE) | |
339 | + return(res) | |
340 | +} | |
341 | + | |
342 | +############This is draw pairs percent on the graph. | |
343 | +AverageNet11 = function(pathname = "/home/zgong001/Documents/Projects/Luminal/3/SS/Pairs-A3-Luminal A-A-B.xlsx", | |
344 | + str = "", | |
345 | + outfile = "/home/zgong001/Documents/dot/out.gv"){ | |
346 | + | |
347 | + library(xlsx) | |
348 | + library(bnlearn) | |
349 | + | |
350 | + res <- read.xlsx(pathname, 1) # read first sheet | |
351 | + res = na.omit(res) | |
352 | + | |
353 | + strD = model2network(as.character(str)) | |
354 | + arcD = arcs(strD) | |
355 | + nodeD = nodes(strD) | |
356 | + arNo = unique(union(arcD[,1], arcD[,2])) | |
357 | + nod = setdiff(nodeD, arNo) | |
358 | + | |
359 | + cat("digraph G {", file=outfile, sep="\n") | |
360 | + | |
361 | + if (length(nod) > 0){ | |
362 | + for(j in 1:length(nod)){ | |
363 | + cat("\t", nod[j], "\n", file=outfile, append=TRUE) | |
364 | + } | |
365 | + } | |
366 | + | |
367 | + p = nrow(arcD) | |
368 | + | |
369 | + for(i in 1:p){ | |
370 | + | |
371 | + mn = paste(arcD[i,1],"->" , arcD[i,2], sep = "") | |
372 | + mn2 = paste(arcD[i,2],"->" , arcD[i,1], sep = "") | |
373 | + s1 = res[which(res[,1]==mn),2] | |
374 | + s2 = res[which(res[,1]==mn2),2] | |
375 | + | |
376 | + if((s1>=0.9999)&(s2<=0.0001)){ | |
377 | + | |
378 | + cat("\t", mn, " [penwidth=", round(s1*10, digits = 2), ",", 'label="', ">99", " (", "~0",')"', "];", "\n", file=outfile, append=TRUE) | |
379 | + | |
380 | + } else if (s1>=0.9999) { | |
381 | + | |
382 | + cat("\t", mn, " [penwidth=", round(s1*10, digits = 2), ",", 'label="', ">99", " (", round(s2*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE) | |
383 | + | |
384 | + } else if (s2<=0.0001) { | |
385 | + | |
386 | + cat("\t", mn, " [penwidth=", round(s1*10, digits = 2), ",", 'label="', round(s1*100 ,digits = 2), " (", "~0",')"', "];", "\n", file=outfile, append=TRUE) | |
387 | + | |
388 | + } else { | |
389 | + cat("\t", mn, " [penwidth=", round(s1*10, digits = 2), ",", 'label="', round(s1*100 ,digits = 2), " (", round(s2*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE) | |
390 | + } | |
391 | + | |
392 | + | |
393 | + } | |
394 | + | |
395 | + cat("\t", 'label="', ' ', "\\l", "Notes:", "\\l", " - >99 represents percentage of 99.99 and above", "\\l", " - ~0 represents percentage of 0.01 and below", "\\l", " - Percentage in the parentheses represents the percentage of an arc that is reversed", '\\l"', ";", "\n", file=outfile, append=TRUE) | |
396 | + cat("}", file=outfile, append=TRUE) | |
397 | + return(res) | |
398 | +} | |
399 | + | |
400 | +ExeAve = function(epathname = "/home/zgong001/Documents/Projects/Luminal/3/SS/Pairs-A3-Luminal A-A-B.xlsx", | |
401 | + strfile = "", | |
402 | + outfile = "/home/zgong001/Documents/dot/"){ | |
403 | + library(xlsx) | |
404 | + strs = read.xlsx(strfile, sheetName = "Structures") # read first sheet | |
405 | + strs = na.omit(strs) | |
406 | + strs = as.data.frame(strs[1:2,1]) | |
407 | + | |
408 | + | |
409 | + for(i in 1:2){ | |
410 | + oun = paste(outfile, "-", i, ".gv", sep = "") | |
411 | + y = AverageNet11(pathname = epathname, | |
412 | + str = as.character(strs[i,1]), | |
413 | + outfile = oun) | |
414 | + } | |
415 | + | |
416 | + return (strs) | |
417 | + | |
418 | +} | |
419 | + | |
420 | +################################################################################################################## | |
421 | +# The following is for the Consensus version 2 | |
422 | +AverageNet21 = function(pathname = "/home/zgong001/Documents/Projects/Luminal/3/SS/Pairs-A3-Luminal A-A-B.xlsx", | |
423 | + str = "", | |
424 | + outfile = "/home/zgong001/Documents/dot/out.gv"){ | |
425 | + | |
426 | + library(xlsx) | |
427 | + library(bnlearn) | |
428 | + | |
429 | + res <- read.xlsx(pathname, 1) # read first sheet | |
430 | + res = na.omit(res) | |
431 | + | |
432 | + | |
433 | + | |
434 | + strD = model2network(as.character(str)) | |
435 | + arcD = arcs(strD) | |
436 | + nodeD = nodes(strD) | |
437 | + arNo = unique(union(arcD[,1], arcD[,2])) | |
438 | + nod = setdiff(nodeD, arNo) | |
439 | + | |
440 | + cat("digraph G {", file=outfile, sep="\n") | |
441 | + | |
442 | + if (length(nod) > 0){ | |
443 | + for(j in 1:length(nod)){ | |
444 | + cat("\t", nod[j], "\n", file=outfile, append=TRUE) | |
445 | + } | |
446 | + } | |
447 | + | |
448 | + p = nrow(arcD) | |
449 | + | |
450 | + for(i in 1:p){ | |
451 | + | |
452 | + mn = paste(arcD[i,1],"->" , arcD[i,2], sep = "") | |
453 | + mn2 = paste(arcD[i,2],"->" , arcD[i,1], sep = "") | |
454 | + s1 = res[which(res[,1]==mn),2] | |
455 | + s2 = res[which(res[,1]==mn2),2] | |
456 | + | |
457 | + if((s1>=0.9999)&(s2<=0.0001)){ | |
458 | + | |
459 | + cat("\t", mn, " [penwidth=", round(s1*10, digits = 2), ",", 'label="', ">99", " (", "~0",')"', "];", "\n", file=outfile, append=TRUE) | |
460 | + | |
461 | + } else if (s1>=0.9999) { | |
462 | + | |
463 | + cat("\t", mn, " [penwidth=", round(s1*10, digits = 2), ",", 'label="', ">99", " (", round(s2*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE) | |
464 | + | |
465 | + } else if (s2<=0.0001) { | |
466 | + | |
467 | + cat("\t", mn, " [penwidth=", round(s1*10, digits = 2), ",", 'label="', round(s1*100 ,digits = 2), " (", "~0",')"', "];", "\n", file=outfile, append=TRUE) | |
468 | + | |
469 | + } else { | |
470 | + | |
471 | + cat("\t", mn, " [penwidth=", round(s1*10, digits = 2), ",", 'label="', round(s1*100 ,digits = 2), " (", round(s2*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE) | |
472 | + | |
473 | + } | |
474 | + | |
475 | + | |
476 | + | |
477 | + } | |
478 | + | |
479 | + NoNA = data.frame() | |
480 | + | |
481 | + arcD = as.data.frame(arcD) | |
482 | + co= combn(nodeD,2) | |
483 | + | |
484 | + | |
485 | + for(j in 1:ncol(co)){ | |
486 | + X = co[1,j] | |
487 | + Y = co[2,j] | |
488 | + | |
489 | + pair_find1 = data.frame(from= X, to=Y) | |
490 | + pair_find2 = data.frame(from= Y, to=X) | |
491 | + | |
492 | + if((nrow(merge(pair_find1,arcD )) == 0) & (nrow(merge(pair_find2,arcD )) == 0)){ | |
493 | + | |
494 | + TX = paste(X,"->", Y, sep = "") | |
495 | + TY = paste(Y,"->", X, sep = "") | |
496 | + t1 = res[which(res[,1]==TX),2] | |
497 | + t2 = res[which(res[,1]==TY),2] | |
498 | + if(t1>t2){ | |
499 | + | |
500 | + if((t1>=0.9999)&(t2<=0.0001)){ | |
501 | + | |
502 | + cat("\t", TX, " [penwidth=", round(t1*10, digits = 2), ",", 'label="', ">99", " (", "~0",')"', "];", "\n", file=outfile, append=TRUE) | |
503 | + | |
504 | + } else if (t1>=0.9999) { | |
505 | + | |
506 | + cat("\t", TX, " [penwidth=", round(t1*10, digits = 2), ",", 'label="', ">99", " (", round(t2*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE) | |
507 | + | |
508 | + } else if (t2<=0.0001) { | |
509 | + | |
510 | + cat("\t", TX, " [penwidth=", round(t1*10, digits = 2), ",", 'label="', round(t1*100 ,digits = 2), " (", "~0",')"', "];", "\n", file=outfile, append=TRUE) | |
511 | + | |
512 | + } else { | |
513 | + | |
514 | + cat("\t", TX, " [penwidth=", round(t1*10, digits = 2), ",", 'label="', round(t1*100 ,digits = 2), " (", round(t2*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE) | |
515 | + | |
516 | + } | |
517 | + | |
518 | + } | |
519 | + else if (t2 >t1){ | |
520 | + | |
521 | + if((t2>=0.9999)&(t1<=0.0001)){ | |
522 | + | |
523 | + cat("\t", TY, " [penwidth=", round(t2*10, digits = 2), ",", 'label="', ">99", " (", "~0",')"', "];", "\n", file=outfile, append=TRUE) | |
524 | + | |
525 | + } else if (t2>=0.9999) { | |
526 | + | |
527 | + cat("\t", TY, " [penwidth=", round(t2*10, digits = 2), ",", 'label="', ">99", " (", round(t1*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE) | |
528 | + | |
529 | + } else if (t1<=0.0001) { | |
530 | + | |
531 | + cat("\t", TY, " [penwidth=", round(t2*10, digits = 2), ",", 'label="', round(t2*100 ,digits = 2), " (", "~0",')"', "];", "\n", file=outfile, append=TRUE) | |
532 | + | |
533 | + } else { | |
534 | + | |
535 | + cat("\t", TY, " [penwidth=", round(t2*10, digits = 2), ",", 'label="', round(t2*100 ,digits = 2), " (", round(t1*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE) | |
536 | + | |
537 | + } | |
538 | + | |
539 | + } | |
540 | + else{ | |
541 | + next | |
542 | + } | |
543 | + | |
544 | + | |
545 | + } | |
546 | + | |
547 | + | |
548 | + } | |
549 | + | |
550 | + cat("\t", 'label="', ' ', "\\l", "Notes:", "\\l", " - >99 represents percentage of 99.99 and above", "\\l", " - ~0 represents percentage of 0.01 and below", "\\l", " - Percentage in the parentheses represents the percentage of an arc that is reversed", '\\l"', ";", "\n", file=outfile, append=TRUE) | |
551 | + cat("}", file=outfile, append=TRUE) | |
552 | + return(arcD) | |
553 | +} | |
0 | 554 | \ No newline at end of file |