1 # -*- coding: utf-8 -*-
2 #Author: Pierre Ratinaud
3 #Copyright (c) 2008-2011 Pierre Ratinaud
7 from chemins import ffr
10 from datetime import datetime
13 log = logging.getLogger('iramuteq.printRscript')
16 def __init__ (self, analyse):
18 self.pathout = analyse.pathout
19 self.analyse = analyse
20 self.parametres = analyse.parametres
21 self.scriptout = self.pathout['temp']
22 self.script = u"#Script genere par IRaMuTeQ - %s" % datetime.now().ctime()
25 self.script = '\n'.join([self.script, txt])
27 def defvar(self, name, value) :
28 self.add(' <- '.join([name, value]))
30 def defvars(self, lvars) :
32 self.defvar(val[0],val[1])
34 def sources(self, lsources) :
35 for source in lsources :
36 self.add('source("%s")' % source)
38 def packages(self, lpks) :
40 self.add('library(%s)' % pk)
44 self.add('load("%s")' % val)
47 with open(self.scriptout, 'w') as f :
51 class chdtxt(PrintRScript) :
55 return str(color).replace(')', ', max=255)')
57 class Alceste2(PrintRScript) :
59 self.sources(['chdfunct'])
61 lvars = [['clnb', `self.analyse.clnb`],
62 ['Contout', '"%s"' % self.pathout['Contout']],
63 ['ContSupOut', '"%s"' % self.pathout['ContSupOut']],
64 ['ContEtOut', '"%s"' % self.pathout['ContEtOut']],
65 ['profileout', '"%s"' % self.pathout['profils.csv']],
66 ['antiout', '"%s"' % self.pathout['antiprofils.csv']],
67 ['chisqtable', '"%s"' % self.pathout['chisqtable.csv']],
68 ['ptable', '"%s"' % self.pathout['ptable.csv']]]
74 # txt = "clnb<-%i\n" % clnb
78 #""" % (RscriptsPath['chdfunct'], DictChdTxtOut['RData'])
80 #dataact<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
81 #datasup<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
82 #dataet<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
83 #""" % (DictChdTxtOut['Contout'], DictChdTxtOut['ContSupOut'], DictChdTxtOut['ContEtOut'])
85 #tablesqrpact<-BuildProf(as.matrix(dataact),n1,clnb)
86 #tablesqrpsup<-BuildProf(as.matrix(datasup),n1,clnb)
87 #tablesqrpet<-BuildProf(as.matrix(dataet),n1,clnb)
90 #PrintProfile(n1,tablesqrpact[4],tablesqrpet[4],tablesqrpact[5],tablesqrpet[5],clnb,"%s","%s",tablesqrpsup[4],tablesqrpsup[5])
91 #""" % (DictChdTxtOut['PROFILE_OUT'], DictChdTxtOut['ANTIPRO_OUT'])
93 #colnames(tablesqrpact[[2]])<-paste('classe',1:clnb,sep=' ')
94 #colnames(tablesqrpact[[1]])<-paste('classe',1:clnb,sep=' ')
95 #colnames(tablesqrpsup[[2]])<-paste('classe',1:clnb,sep=' ')
96 #colnames(tablesqrpsup[[1]])<-paste('classe',1:clnb,sep=' ')
97 #colnames(tablesqrpet[[2]])<-paste('classe',1:clnb,sep=' ')
98 #colnames(tablesqrpet[[1]])<-paste('classe',1:clnb,sep=' ')
99 #chistabletot<-rbind(tablesqrpact[2][[1]],tablesqrpsup[2][[1]])
100 #chistabletot<-rbind(chistabletot,tablesqrpet[2][[1]])
101 #ptabletot<-rbind(tablesqrpact[1][[1]],tablesqrpet[1][[1]])
104 #write.csv2(chistabletot,file="%s")
105 #write.csv2(ptabletot,file="%s")
107 #write.csv2(gbcluster,file="%s")
108 #""" % (DictChdTxtOut['chisqtable'], DictChdTxtOut['ptable'], DictChdTxtOut['SbyClasseOut'])
112 def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, libsvdc = False, libsvdc_path = None, R_max_mem = False):
118 """ % (RscriptPath['CHD'], RscriptPath['chdtxt'], RscriptPath['anacor'], RscriptPath['Rgraph'])
131 """ % ffr(libsvdc_path)
140 data1 <- readMM("%s")
141 data1 <- as(data1, "dgCMatrix")
142 row.names(data1) <- 1:nrow(data1)
143 """ % DicoPath['TableUc1']
145 if classif_mode == 0:
147 data2 <- readMM("%s")
148 data2 <- as(data2, "dgCMatrix")
149 row.names(data2) <- 1:nrow(data2)
150 """ % DicoPath['TableUc2']
152 chd1<-CHD(data1, x = nbt, libsvdc = libsvdc, libsvdc.path = libsvdc.path)
155 if classif_mode == 0:
157 chd2<-CHD(data2, x = nbt, libsvdc = libsvdc, libsvdc.path = libsvdc.path)
166 listuce1<-read.csv2("%s")
167 """ % DicoPath['listeuce1']
169 if classif_mode == 0:
171 listuce2<-read.csv2("%s")
172 """ % DicoPath['listeuce2']
178 if classif_mode == 0:
183 chd.result <- Rchdtxt("%s",mincl=%i,classif_mode=%i, nbt = nbt)
185 classeuce1 <- chd.result$cuce1
186 classeuce2 <- chd.result$cuce2
187 """ % (DicoPath['uce'], mincl, classif_mode)
190 tree.tot1 <- make_tree_tot(chd1)
191 # open_file_graph("%s", widt = 600, height=400)
192 # plot(tree.tot1$tree.cl)
194 """%DicoPath['arbre1']
196 if classif_mode == 0:
198 tree.tot2 <- make_tree_tot(chd2)
199 # open_file_graph("%s", width = 600, height=400)
200 # plot(tree.tot2$tree.cl)
202 """ % DicoPath['arbre2']
205 tree.cut1 <- make_dendro_cut_tuple(tree.tot1$dendro_tuple, chd.result$coord_ok, classeuce1, 1, nbt)
206 save(tree.cut1, file="%s")
207 classes<-n1[,ncol(n1)]
208 open_file_graph("%s", width = 600, height=400)
209 plot.dendropr(tree.cut1$tree.cl,classes)
210 open_file_graph("%s", width = 600, height=400)
211 plot(tree.cut1$dendro_tot_cl)
213 """ % (DicoPath['Rdendro'], DicoPath['dendro1'], DicoPath['arbre1'])
215 if classif_mode == 0:
217 tree.cut2 <- make_dendro_cut_tuple(tree.tot2$dendro_tuple, chd.result$coord_ok, classeuce2, 2, nbt)
218 open_file_graph("%s", width = 600, height=400)
219 plot(tree.cut2$tree.cl)
221 open_file_graph("%s", width = 600, height=400)
222 plot(tree.cut1$dendro_tot_cl)
224 """ % (DicoPath['dendro2'], DicoPath['arbre2'])
227 save.image(file="%s")
228 """ % DicoPath['RData']
229 fileout = open(DicoPath['Rchdtxt'], 'w')
233 def RPamTxt(corpus, RscriptPath):
234 DicoPath = corpus.dictpathout
235 param = corpus.parametre
239 """ % (RscriptPath['pamtxt'])
242 """ % (RscriptPath['Rgraph'])
244 result <- pamtxt("%s", "%s", "%s", method = "%s", clust_type = "%s", clnb = %i)
246 """ % (DicoPath['TableUc1'], DicoPath['listeuce1'], DicoPath['uce'], param['method'], param['cluster_type'], param['nbcl'] )
248 open_file_graph("%s", width=400, height=400)
251 """ % (DicoPath['arbre1'])
253 save.image(file="%s")
254 """ % DicoPath['RData']
255 fileout = open(DicoPath['Rchdtxt'], 'w')
260 def RchdQuest(DicoPath, RscriptPath, nbcl = 10, mincl = 10):
266 """ % (RscriptPath['CHD'], RscriptPath['chdquest'], RscriptPath['anacor'],RscriptPath['Rgraph'])
274 chd.result<-Rchdquest("%s","%s","%s", nbt = nbt, mincl = mincl)
276 classeuce1 <- chd.result$cuce1
277 """ % (DicoPath['Act01'], DicoPath['listeuce1'], DicoPath['uce'])
280 tree_tot1 <- make_tree_tot(chd.result$chd)
281 open_file_graph("%s", width = 600, height=400)
282 plot(tree_tot1$tree.cl)
284 """%DicoPath['arbre1']
287 tree_cut1 <- make_dendro_cut_tuple(tree_tot1$dendro_tuple, chd.result$coord_ok, classeuce1, 1, nbt)
288 tree.cut1 <- tree_cut1
289 save(tree.cut1, file="%s")
290 open_file_graph("%s", width = 600, height=400)
291 classes<-n1[,ncol(n1)]
292 plot.dendropr(tree_cut1$tree.cl,classes)
293 """ % (DicoPath['Rdendro'],DicoPath['dendro1'])
296 save.image(file="%s")
297 """ % DicoPath['RData']
298 fileout = open(DicoPath['Rchdquest'], 'w')
302 def AlcesteTxtProf(DictChdTxtOut, RscriptsPath, clnb, taillecar):
303 txt = "clnb<-%i\n" % clnb
307 """ % (RscriptsPath['chdfunct'], DictChdTxtOut['RData'])
309 dataact<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
310 datasup<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
311 dataet<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
312 """ % (DictChdTxtOut['Contout'], DictChdTxtOut['ContSupOut'], DictChdTxtOut['ContEtOut'])
314 tablesqrpact<-BuildProf(as.matrix(dataact),n1,clnb)
315 tablesqrpsup<-BuildProf(as.matrix(datasup),n1,clnb)
316 tablesqrpet<-BuildProf(as.matrix(dataet),n1,clnb)
319 PrintProfile(n1,tablesqrpact[4],tablesqrpet[4],tablesqrpact[5],tablesqrpet[5],clnb,"%s","%s",tablesqrpsup[4],tablesqrpsup[5])
320 """ % (DictChdTxtOut['PROFILE_OUT'], DictChdTxtOut['ANTIPRO_OUT'])
322 colnames(tablesqrpact[[2]])<-paste('classe',1:clnb,sep=' ')
323 colnames(tablesqrpact[[1]])<-paste('classe',1:clnb,sep=' ')
324 colnames(tablesqrpsup[[2]])<-paste('classe',1:clnb,sep=' ')
325 colnames(tablesqrpsup[[1]])<-paste('classe',1:clnb,sep=' ')
326 colnames(tablesqrpet[[2]])<-paste('classe',1:clnb,sep=' ')
327 colnames(tablesqrpet[[1]])<-paste('classe',1:clnb,sep=' ')
328 chistabletot<-rbind(tablesqrpact[2][[1]],tablesqrpsup[2][[1]])
329 chistabletot<-rbind(chistabletot,tablesqrpet[2][[1]])
330 ptabletot<-rbind(tablesqrpact[1][[1]],tablesqrpet[1][[1]])
333 write.csv2(chistabletot,file="%s")
334 write.csv2(ptabletot,file="%s")
336 write.csv2(gbcluster,file="%s")
337 """ % (DictChdTxtOut['chisqtable'], DictChdTxtOut['ptable'], DictChdTxtOut['SbyClasseOut'])
341 colnames(dataact)<-paste('classe',1:clnb,sep=' ')
342 colnames(datasup)<-paste('classe',1:clnb,sep=' ')
343 colnames(dataet)<-paste('classe',1:clnb,sep=' ')
344 rowtot<-nrow(dataact)+nrow(dataet)+nrow(datasup)
345 afctable<-rbind(as.matrix(dataact),as.matrix(datasup))
346 afctable<-rbind(afctable,as.matrix(dataet))
347 colnames(afctable)<-paste('classe',1:clnb,sep=' ')
348 afc<-ca(afctable,suprow=((nrow(dataact)+1):rowtot),nd=(ncol(afctable)-1))
349 debsup<-nrow(dataact)+1
350 debet<-nrow(dataact)+nrow(datasup)+1
352 afc<-AddCorrelationOk(afc)
354 #FIXME : split this!!!
357 """ % RscriptsPath['Rgraph']
360 afc <- summary.ca.dm(afc)
361 afc_table <- create_afc_table(afc)
362 write.csv2(afc_table$facteur, file = "%s")
363 write.csv2(afc_table$colonne, file = "%s")
364 write.csv2(afc_table$ligne, file = "%s")
365 """ % (DictChdTxtOut['afc_facteur'], DictChdTxtOut['afc_col'], DictChdTxtOut['afc_row'])
368 xlab <- paste('facteur 1 - ', round(afc$facteur[1,2],2), sep = '')
369 ylab <- paste('facteur 2 - ', round(afc$facteur[2,2],2), sep = '')
370 xlab <- paste(xlab, ' %', sep = '')
371 ylab <- paste(ylab, ' %', sep = '')
378 PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
379 """ % (DictChdTxtOut['AFC2DL_OUT'])
381 PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab)
382 """ % (DictChdTxtOut['AFC2DSL_OUT'])
384 PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debet, fin=fin, xlab = xlab, ylab = ylab)
385 """ % (DictChdTxtOut['AFC2DEL_OUT'])
387 PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='coord', xlab = xlab, ylab = ylab)
388 """ % (DictChdTxtOut['AFC2DCL_OUT'])
390 PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
391 PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab)
392 PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=debet, fin=fin, xlab = xlab, ylab = ylab)
393 PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='crl', xlab = xlab, ylab = ylab)
394 """ % (DictChdTxtOut['AFC2DCoul'], DictChdTxtOut['AFC2DCoulSup'], DictChdTxtOut['AFC2DCoulEt'], DictChdTxtOut['AFC2DCoulCl'])
403 save.image(file="%s")
404 """ % DictChdTxtOut['RData']
405 file = open(DictChdTxtOut['RTxtProfGraph'], 'w')
410 def write_afc_graph(self):
411 if self.param['over'] : over = 'TRUE'
412 else : over = 'FALSE'
414 if self.param['do_select_nb'] : do_select_nb = 'TRUE'
415 else : do_select_nb = 'FALSE'
417 if self.param['do_select_chi'] : do_select_chi = 'TRUE'
418 else : do_select_chi = 'FALSE'
420 if self.param['cex_txt'] : cex_txt = 'TRUE'
421 else : cex_txt = 'FALSE'
423 if self.param['tchi'] : tchi = 'TRUE'
424 else : tchi = 'FALSE'
426 with open(self.RscriptsPath['afc_graph'], 'r') as f:
429 # self.DictPathOut['RData'], \
430 scripts = txt % (self.RscriptsPath['Rgraph'],\
431 self.param['typegraph'], \
432 self.param['what'], \
433 self.param['facteur'][0],\
434 self.param['facteur'][1], \
435 self.param['facteur'][2], \
437 over, do_select_nb, \
438 self.param['select_nb'], \
440 self.param['select_chi'], \
442 self.param['txt_min'], \
443 self.param['txt_max'], \
445 self.param['width'], \
446 self.param['height'],\
447 self.param['taillecar'], \
448 self.param['alpha'], \
449 self.param['film'], \
451 self.param['tchi_min'],\
452 self.param['tchi_max'],\
453 ffr(os.path.dirname(self.fileout)))
456 def print_simi3d(self):
457 simi3d = self.parent.simi3dpanel
458 txt = '#Fichier genere par Iramuteq'
459 if simi3d.movie.GetValue() :
460 movie = "'" + ffr(os.path.dirname(self.DictPathOut['RData'])) + "'"
463 if self.section == 'chd_dist_quest' :
468 dm<-read.csv2("%s",row.names=1,header = %s)
470 """ % (self.DictPathOut['Contout'], header, self.DictPathOut['RData'])
474 """ % self.parent.RscriptsPath['Rgraph']
478 make.simi.afc(dm,chistabletot, lim=%i, alpha = %.2f, movie = %s)
479 """ % (simi3d.spin_1.GetValue(), float(simi3d.slider_1.GetValue())/100, movie)
480 tmpfile = tempfile.mktemp(dir=self.parent.TEMPDIR)
481 tmp = open(tmpfile,'w')
486 def dendroandbarplot(table, rownames, colnames, rgraph, tmpgraph, intxt = False, dendro=False) :
488 txttable = 'c(' + ','.join([','.join(line) for line in table]) + ')'
489 rownb = len(rownames)
490 rownames = 'c("' + '","'.join(rownames) + '")'
491 colnames = 'c("' + '","'.join(colnames) + '")'
495 di <- matrix(data=%s, nrow=%i, byrow = TRUE)
498 """ % (txttable, rownb, rownames, colnames)
505 height <- (30*ncol(di)) + (15*nrow(di))
506 height <- ifelse(height <= 400, 400, height)
508 open_file_graph("%s", width=width, height=height)
509 plot.dendro.lex(tree.cut1$tree.cl, di)
510 """ % (ffr(dendro),ffr(rgraph), ffr(tmpgraph))
513 def barplot(table, rownames, colnames, rgraph, tmpgraph, intxt = False) :
515 txttable = 'c(' + ','.join([','.join(line) for line in table]) + ')'
516 #width = 100 + (15 * len(rownames)) + (100 * len(colnames))
517 #height = len(rownames) * 15
518 rownb = len(rownames)
521 rownames = 'c("' + '","'.join(rownames) + '")'
522 colnames = 'c("' + '","'.join(colnames) + '")'
527 di <- matrix(data=%s, nrow=%i, byrow = TRUE)
528 di[is.na(di)] <- max(di, na.rm=TRUE) + 2
531 """ % (txttable, rownb, rownames, colnames)
536 color = rainbow(nrow(di))
537 width <- 100 + (20*length(rownames(di))) + (100 * length(colnames(di)))
538 height <- nrow(di) * 15
539 if (height < 400) { height <- 400}
540 open_file_graph("%s",width = width, height = height)
542 layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(7)))
544 coord <- barplot(as.matrix(di), beside = TRUE, col = color, space = c(0.1,0.6))
549 lcoord <- apply(cc, 1, mean)
552 amp <- abs(max(di) - min(di))
559 d <- signif(amp%%/%%10,1)
564 if ((i/d) == (i%%/%%d)) {
569 plot(0, axes = FALSE, pch = '')
570 legend(x = 'center' , rownames(di), fill = color)
572 """ % (rgraph, ffr(tmpgraph))
575 #def RAfcUci(DictAfcUciOut, nd=2, RscriptsPath='', PARCEX='0.8'):
581 # dataact<-read.csv2("%s")
582 # """ % (DictAfcUciOut['TableCont'])#, encoding)
584 # datasup<-read.csv2("%s")
585 # """ % (DictAfcUciOut['TableSup'])#, encoding)
587 # dataet<-read.csv2("%s")
588 # """ % (DictAfcUciOut['TableEt'])#, encoding)
590 # datatotsup<-cbind(dataact,datasup)
591 # datatotet<-cbind(dataact,dataet)
592 # afcact<-ca(dataact,nd=nd)
593 # afcsup<-ca(datatotsup,supcol=((ncol(dataact)+1):ncol(datatotsup)),nd=nd)
594 # afcet<-ca(datatotet,supcol=((ncol(dataact)+1):ncol(datatotet)),nd=nd)
595 # afctot<-afcsup$colcoord
596 # rownames(afctot)<-afcsup$colnames
597 # colnames(afctot)<-paste('coord. facteur',1:nd,sep=' ')
598 # afctot<-cbind(afctot,mass=afcsup$colmass)
599 # afctot<-cbind(afctot,distance=afcsup$coldist)
600 # afctot<-cbind(afctot,intertie=afcsup$colinertia)
601 # rcolet<-afcet$colsup
602 # afctmp<-afcet$colcoord[rcolet,]
603 # rownames(afctmp)<-afcet$colnames[rcolet]
604 # afctmp<-cbind(afctmp,afcet$colmass[rcolet])
605 # afctmp<-cbind(afctmp,afcet$coldist[rcolet])
606 # afctmp<-cbind(afctmp,afcet$colinertia[rcolet])
607 # afctot<-rbind(afctot,afctmp)
608 # write.csv2(afctot,file = "%s")
610 # """ % (DictAfcUciOut['afc_row'], RscriptsPath['Rgraph'])
616 # PlotAfc(afcet,filename="%s",toplot=c%s, PARCEX=PARCEX)
617 # """ % (DictAfcUciOut['AfcColAct'], "('none','active')")
619 # PlotAfc(afcsup,filename="%s",toplot=c%s, PARCEX=PARCEX)
620 # """ % (DictAfcUciOut['AfcColSup'], "('none','passive')")
621 # txt += """PlotAfc(afcet,filename="%s", toplot=c%s, PARCEX=PARCEX)
622 # """ % (DictAfcUciOut['AfcColEt'], "('none','passive')")
624 # PlotAfc(afcet,filename="%s", toplot=c%s, PARCEX=PARCEX)
625 # """ % (DictAfcUciOut['AfcRow'], "('all','none')")
626 # f = open(DictAfcUciOut['Rafcuci'], 'w')
630 class PrintSimiScript(PrintRScript) :
631 def make_script(self) :
633 self.packages(['igraph', 'proxy', 'Matrix'])
634 self.sources([self.analyse.parent.RscriptsPath['simi'], self.analyse.parent.RscriptsPath['Rgraph']])
639 """ % (self.pathout['mat01.csv'], self.pathout['actives.csv'], self.pathout['selected.csv'])
642 cn <- read.table(cn.path, sep=';', quote='"')
643 colnames(dm) <- cn[,1]
644 sel.col <- read.csv2(selected.col)
645 dm <- dm[, sel.col[,1] + 1]
648 if self.parametres['coeff'] == 0 :
658 if self.parametres['coeff'] == 1 :
662 mat <- simil(dm, method = 'Russel', diag = TRUE, upper = TRUE, by_rows = FALSE)
664 elif self.analyse.indices[self.parametres['coeff']] == 'binomial' :
670 elif self.parametres['coeff'] != 0 :
671 method = self.analyse.indices[self.parametres['coeff']]
674 mat <- simil(dm, method = method, diag = TRUE, upper = TRUE, by_rows = FALSE)
675 """ % self.analyse.indices[self.parametres['coeff']]
677 mat <- as.matrix(stats::as.dist(mat,diag=TRUE,upper=TRUE))
679 mat[is.infinite(mat)] <- 0
681 if self.parametres['layout'] == 0 : layout = 'random'
682 if self.parametres['layout'] == 1 : layout = 'circle'
683 if self.parametres['layout'] == 2 : layout = 'frutch'
684 if self.parametres['layout'] == 3 : layout = 'kawa'
685 if self.parametres['layout'] == 4 : layout = 'graphopt'
688 if self.parametres['type_graph'] == 0 : type = 'tkplot'
689 if self.parametres['type_graph'] == 1 :
692 dirout = os.path.dirname(self.pathout['mat01'])
693 while os.path.exists(os.path.join(dirout,'graph_simi_'+str(graphnb)+'.png')):
695 self.filename = ffr(os.path.join(dirout,'graph_simi_'+str(graphnb)+'.png'))
696 if self.parametres['type_graph'] == 2 : type = 'rgl'
698 if self.parametres['arbremax'] :
700 self.txtgraph += ' - arbre maximum'
701 else : arbremax = 'FALSE'
703 if self.parametres['coeff_tv'] :
704 coeff_tv = self.parametres['coeff_tv_nb']
705 tvminmax = 'c(NULL,NULL)'
706 elif not self.parametres['coeff_tv'] or self.parametres.get('sformchi', False) :
708 tvminmax = 'c(%i, %i)' %(self.parametres['tvmin'], self.parametres['tvmax'])
709 if self.parametres['coeff_te'] : coeff_te = 'c(%i,%i)' % (self.parametres['coeff_temin'], self.parametres['coeff_temax'])
710 else : coeff_te = 'NULL'
712 if self.parametres['vcex'] or self.parametres.get('cexfromchi', False) :
713 vcexminmax = 'c(%i/10,%i/10)' % (self.parametres['vcexmin'],self.parametres['vcexmax'])
715 vcexminmax = 'c(NULL,NULL)'
716 if not self.parametres['label_v'] : label_v = 'FALSE'
717 else : label_v = 'TRUE'
719 if not self.parametres['label_e'] : label_e = 'FALSE'
720 else : label_e = 'TRUE'
722 if self.parametres['seuil_ok'] : seuil = str(self.parametres['seuil'])
723 else : seuil = 'NULL'
725 cols = str(self.parametres['cols']).replace(')',', max=255)')
726 cola = str(self.parametres['cola']).replace(')',',max=255)')
736 """ % self.parametres['cex']
738 if self.parametres['film'] :
741 """ % self.pathout['film']
753 """ % (label_v, label_e)
761 """ % (self.parametres['width'], self.parametres['height'])
762 if self.parametres['keep_coord'] :
764 coords <- try(coords, TRUE)
765 if (!is.matrix(coords)) {
775 """ % self.parametres['alpha']
778 """ % self.parametres['alpha']
779 #############################################
780 if self.parametres.get('bystar',False) :
784 for i,et in enumerate(self.tableau.etline) :
787 """ % (i+1, ','.join(et[1:]))
790 """ % ("','".join([val[0] for val in self.tableau.etline]))
794 for (i in 1:length(unetoile)) {
797 if (length(tosum) > 1) {
798 fsum <- cbind(fsum, colSums(dm[tosum,]))
800 fsum <- cbind(fsum, dm[tosum,])
804 lex <- AsLexico2(fsum, chip=TRUE)
805 dcol <- apply(lex[[4]],1,which.max)
806 toblack <- apply(lex[[4]],1,max)
807 gcol <- rainbow(length(unetoile))
809 vertex.label.color <- gcol[dcol]
810 vertex.label.color[which(toblack <= 3.84)] <- 'black'
811 leg <- list(unetoile=unetoile, gcol=gcol)
812 cols <- vertex.label.color
813 chivertex.size <- norm.vec(toblack, vcexminmax[1], vcexminmax[2])
815 """ % (self.parent.RscriptsPath['chdfunct'])
818 vertex.label.color <- 'black'
822 #############################################
826 # g.ori <- graph.adjacency(mat, mode='lower', weighted = TRUE)
827 # w.ori <- E(g.ori)$weight
829 # if (method == 'cooc') {
830 # E(g.ori)$weight <- 1 / w.ori
832 # E(g.ori)$weigth <- 1 - w.ori
834 # g.max <- minimum.spanning.tree(g.ori)
835 # if (method == 'cooc') {
836 # E(g.max)$weight <- 1 / E(g.max)$weight
838 # E(g.max)$weight <- 1 - E(g.max)$weight
847 x <- list(mat = mat, eff = eff)
848 graph.simi <- do.simi(x, method='%s', seuil = seuil, p.type = '%s', layout.type = '%s', max.tree = %s, coeff.vertex=%s, coeff.edge = %s, minmaxeff = minmaxeff, vcexminmax = vcexminmax, cex = cex, coords = coords)
849 """ % (method, type, layout, arbremax, coeff_tv, coeff_te)
851 if self.parametres.get('bystar',False) :
852 if self.parametres.get('cexfromchi', False) :
854 label.cex<-chivertex.size
860 if self.parametres.get('sfromchi', False) :
862 vertex.size <- norm.vec(toblack, minmaxeff[1], minmaxeff[2])
873 lchi <- read.table("%s")
876 if 'selected_col' in dir(self.tableau) :
880 if tmpchi and self.parametres.get('cexfromchi', False) :
882 label.cex <- norm.vec(lchi, vcexminmax[1], vcexminmax[2])
886 if (is.null(vcexminmax[1])) {
889 label.cex <- graph.simi$label.cex
892 if tmpchi and self.parametres.get('sfromchi', False) :
894 vertex.size <- norm.vec(lchi, minmaxeff[1], minmaxeff[2])
898 if (is.null(minmaxeff[1])) {
901 vertex.size <- graph.simi$eff
904 txt += """ vertex.size <- NULL """
906 coords <- plot.simi(graph.simi, p.type='%s',filename="%s", vertex.label = label.v, edge.label = label.e, vertex.col = cols, vertex.label.color = vertex.label.color, vertex.label.cex=label.cex, vertex.size = vertex.size, edge.col = cola, leg=leg, width = width, height = height, alpha = alpha, movie = film)
907 save.image(file="%s")
908 """ % (type, self.filename, self.pathout['RData'])
913 class WordCloudRScript(PrintRScript) :
914 def make_script(self) :
915 self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
916 self.packages(['wordcloud'])
917 bg_col = Rcolor(self.parametres['col_bg'])
918 txt_col = Rcolor(self.parametres['col_text'])
920 act <- read.csv2("%s", header = FALSE, row.names=1, sep='\t')
921 selected.col <- read.table("%s")
922 toprint <- act[selected.col[,1] + 1,]
923 open_file_graph("%s", width = %i, height = %i)
925 wordcloud(row.names(toprint), toprint[,1], scale=c(%f,%f), random.order=FALSE, colors=rgb%s)
927 """ % (ffr(self.analyse.pathout['actives_eff.csv']), ffr(self.analyse.pathout['selected.csv']),
928 ffr(self.parametres['graphout']), self.parametres['width'], self.parametres['height'], bg_col, self.parametres['maxcex'], self.parametres['mincex'], txt_col)