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']
151 #log.info('ATTENTION ############# MODEPATATE ####################')
153 chd1<-CHD(data1, x = nbt, mode.patate = FALSE, libsvdc = libsvdc, libsvdc.path = libsvdc.path)
156 if classif_mode == 0:
158 chd2<-CHD(data2, x = nbt, libsvdc = libsvdc, libsvdc.path = libsvdc.path)
167 listuce1<-read.csv2("%s")
168 """ % DicoPath['listeuce1']
170 if classif_mode == 0:
172 listuce2<-read.csv2("%s")
173 """ % DicoPath['listeuce2']
179 if classif_mode == 0:
184 chd.result <- Rchdtxt("%s",mincl=%i,classif_mode=%i, nbt = nbt)
186 classeuce1 <- chd.result$cuce1
187 classeuce2 <- chd.result$cuce2
188 """ % (DicoPath['uce'], mincl, classif_mode)
191 tree.tot1 <- make_tree_tot(chd1)
192 # open_file_graph("%s", widt = 600, height=400)
193 # plot(tree.tot1$tree.cl)
195 """%DicoPath['arbre1']
197 if classif_mode == 0:
199 tree.tot2 <- make_tree_tot(chd2)
200 # open_file_graph("%s", width = 600, height=400)
201 # plot(tree.tot2$tree.cl)
203 """ % DicoPath['arbre2']
206 tree.cut1 <- make_dendro_cut_tuple(tree.tot1$dendro_tuple, chd.result$coord_ok, classeuce1, 1, nbt)
207 save(tree.cut1, file="%s")
208 classes<-n1[,ncol(n1)]
209 open_file_graph("%s", width = 600, height=400)
210 plot.dendropr(tree.cut1$tree.cl,classes)
211 open_file_graph("%s", width = 600, height=400)
212 plot(tree.cut1$dendro_tot_cl)
214 """ % (DicoPath['Rdendro'], DicoPath['dendro1'], DicoPath['arbre1'])
216 if classif_mode == 0:
218 tree.cut2 <- make_dendro_cut_tuple(tree.tot2$dendro_tuple, chd.result$coord_ok, classeuce2, 2, nbt)
219 open_file_graph("%s", width = 600, height=400)
220 plot(tree.cut2$tree.cl)
222 open_file_graph("%s", width = 600, height=400)
223 plot(tree.cut1$dendro_tot_cl)
225 """ % (DicoPath['dendro2'], DicoPath['arbre2'])
228 save.image(file="%s")
229 """ % DicoPath['RData']
230 fileout = open(DicoPath['Rchdtxt'], 'w')
234 def RPamTxt(corpus, RscriptPath):
235 DicoPath = corpus.dictpathout
236 param = corpus.parametre
240 """ % (RscriptPath['pamtxt'])
243 """ % (RscriptPath['Rgraph'])
245 result <- pamtxt("%s", "%s", "%s", method = "%s", clust_type = "%s", clnb = %i)
247 """ % (DicoPath['TableUc1'], DicoPath['listeuce1'], DicoPath['uce'], param['method'], param['cluster_type'], param['nbcl'] )
249 open_file_graph("%s", width=400, height=400)
252 """ % (DicoPath['arbre1'])
254 save.image(file="%s")
255 """ % DicoPath['RData']
256 fileout = open(DicoPath['Rchdtxt'], 'w')
261 def RchdQuest(DicoPath, RscriptPath, nbcl = 10, mincl = 10):
267 """ % (RscriptPath['CHD'], RscriptPath['chdquest'], RscriptPath['anacor'],RscriptPath['Rgraph'])
275 chd.result<-Rchdquest("%s","%s","%s", nbt = nbt, mincl = mincl)
277 classeuce1 <- chd.result$cuce1
278 """ % (DicoPath['Act01'], DicoPath['listeuce1'], DicoPath['uce'])
281 tree_tot1 <- make_tree_tot(chd.result$chd)
282 open_file_graph("%s", width = 600, height=400)
283 plot(tree_tot1$tree.cl)
285 """%DicoPath['arbre1']
288 tree_cut1 <- make_dendro_cut_tuple(tree_tot1$dendro_tuple, chd.result$coord_ok, classeuce1, 1, nbt)
289 tree.cut1 <- tree_cut1
290 save(tree.cut1, file="%s")
291 open_file_graph("%s", width = 600, height=400)
292 classes<-n1[,ncol(n1)]
293 plot.dendropr(tree_cut1$tree.cl,classes)
294 """ % (DicoPath['Rdendro'],DicoPath['dendro1'])
297 save.image(file="%s")
298 """ % DicoPath['RData']
299 fileout = open(DicoPath['Rchdquest'], 'w')
303 def AlcesteTxtProf(DictChdTxtOut, RscriptsPath, clnb, taillecar):
304 txt = "clnb<-%i\n" % clnb
308 """ % (RscriptsPath['chdfunct'], DictChdTxtOut['RData'])
310 dataact<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
311 datasup<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
312 dataet<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
313 """ % (DictChdTxtOut['Contout'], DictChdTxtOut['ContSupOut'], DictChdTxtOut['ContEtOut'])
315 tablesqrpact<-BuildProf(as.matrix(dataact),n1,clnb)
316 tablesqrpsup<-BuildProf(as.matrix(datasup),n1,clnb)
317 tablesqrpet<-BuildProf(as.matrix(dataet),n1,clnb)
320 PrintProfile(n1,tablesqrpact[4],tablesqrpet[4],tablesqrpact[5],tablesqrpet[5],clnb,"%s","%s",tablesqrpsup[4],tablesqrpsup[5])
321 """ % (DictChdTxtOut['PROFILE_OUT'], DictChdTxtOut['ANTIPRO_OUT'])
323 colnames(tablesqrpact[[2]])<-paste('classe',1:clnb,sep=' ')
324 colnames(tablesqrpact[[1]])<-paste('classe',1:clnb,sep=' ')
325 colnames(tablesqrpsup[[2]])<-paste('classe',1:clnb,sep=' ')
326 colnames(tablesqrpsup[[1]])<-paste('classe',1:clnb,sep=' ')
327 colnames(tablesqrpet[[2]])<-paste('classe',1:clnb,sep=' ')
328 colnames(tablesqrpet[[1]])<-paste('classe',1:clnb,sep=' ')
329 chistabletot<-rbind(tablesqrpact[2][[1]],tablesqrpsup[2][[1]])
330 chistabletot<-rbind(chistabletot,tablesqrpet[2][[1]])
331 ptabletot<-rbind(tablesqrpact[1][[1]],tablesqrpet[1][[1]])
334 write.csv2(chistabletot,file="%s")
335 write.csv2(ptabletot,file="%s")
337 write.csv2(gbcluster,file="%s")
338 """ % (DictChdTxtOut['chisqtable'], DictChdTxtOut['ptable'], DictChdTxtOut['SbyClasseOut'])
342 colnames(dataact)<-paste('classe',1:clnb,sep=' ')
343 colnames(datasup)<-paste('classe',1:clnb,sep=' ')
344 colnames(dataet)<-paste('classe',1:clnb,sep=' ')
345 rowtot<-nrow(dataact)+nrow(dataet)+nrow(datasup)
346 afctable<-rbind(as.matrix(dataact),as.matrix(datasup))
347 afctable<-rbind(afctable,as.matrix(dataet))
348 colnames(afctable)<-paste('classe',1:clnb,sep=' ')
349 afc<-ca(afctable,suprow=((nrow(dataact)+1):rowtot),nd=(ncol(afctable)-1))
350 debsup<-nrow(dataact)+1
351 debet<-nrow(dataact)+nrow(datasup)+1
353 afc<-AddCorrelationOk(afc)
355 #FIXME : split this!!!
358 """ % RscriptsPath['Rgraph']
361 afc <- summary.ca.dm(afc)
362 afc_table <- create_afc_table(afc)
363 write.csv2(afc_table$facteur, file = "%s")
364 write.csv2(afc_table$colonne, file = "%s")
365 write.csv2(afc_table$ligne, file = "%s")
366 """ % (DictChdTxtOut['afc_facteur'], DictChdTxtOut['afc_col'], DictChdTxtOut['afc_row'])
369 xlab <- paste('facteur 1 - ', round(afc$facteur[1,2],2), sep = '')
370 ylab <- paste('facteur 2 - ', round(afc$facteur[2,2],2), sep = '')
371 xlab <- paste(xlab, ' %', sep = '')
372 ylab <- paste(ylab, ' %', sep = '')
379 PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
380 """ % (DictChdTxtOut['AFC2DL_OUT'])
382 PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab)
383 """ % (DictChdTxtOut['AFC2DSL_OUT'])
385 PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debet, fin=fin, xlab = xlab, ylab = ylab)
386 """ % (DictChdTxtOut['AFC2DEL_OUT'])
388 PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='coord', xlab = xlab, ylab = ylab)
389 """ % (DictChdTxtOut['AFC2DCL_OUT'])
391 PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
392 PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab)
393 PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=debet, fin=fin, xlab = xlab, ylab = ylab)
394 PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='crl', xlab = xlab, ylab = ylab)
395 """ % (DictChdTxtOut['AFC2DCoul'], DictChdTxtOut['AFC2DCoulSup'], DictChdTxtOut['AFC2DCoulEt'], DictChdTxtOut['AFC2DCoulCl'])
404 save.image(file="%s")
405 """ % DictChdTxtOut['RData']
406 file = open(DictChdTxtOut['RTxtProfGraph'], 'w')
411 def write_afc_graph(self):
412 if self.param['over'] : over = 'TRUE'
413 else : over = 'FALSE'
415 if self.param['do_select_nb'] : do_select_nb = 'TRUE'
416 else : do_select_nb = 'FALSE'
418 if self.param['do_select_chi'] : do_select_chi = 'TRUE'
419 else : do_select_chi = 'FALSE'
421 if self.param['do_select_chi_classe'] : do_select_chi_classe = 'TRUE'
422 else : do_select_chi_classe = 'FALSE'
424 if self.param['cex_txt'] : cex_txt = 'TRUE'
425 else : cex_txt = 'FALSE'
427 if self.param['tchi'] : tchi = 'TRUE'
428 else : tchi = 'FALSE'
430 with open(self.RscriptsPath['afc_graph'], 'r') as f:
433 # self.DictPathOut['RData'], \
434 scripts = txt % (self.RscriptsPath['Rgraph'],\
435 self.param['typegraph'], \
436 self.param['what'], \
437 self.param['facteur'][0],\
438 self.param['facteur'][1], \
439 self.param['facteur'][2], \
441 over, do_select_nb, \
442 self.param['select_nb'], \
444 self.param['select_chi'], \
445 do_select_chi_classe, \
446 self.param['nbchic'], \
448 self.param['txt_min'], \
449 self.param['txt_max'], \
451 self.param['width'], \
452 self.param['height'],\
453 self.param['taillecar'], \
454 self.param['alpha'], \
455 self.param['film'], \
457 self.param['tchi_min'],\
458 self.param['tchi_max'],\
459 ffr(os.path.dirname(self.fileout)))
462 def print_simi3d(self):
463 simi3d = self.parent.simi3dpanel
464 txt = '#Fichier genere par Iramuteq'
465 if simi3d.movie.GetValue() :
466 movie = "'" + ffr(os.path.dirname(self.DictPathOut['RData'])) + "'"
470 #if self.corpus.parametres['type'] == 'corpus' :
476 dm<-read.csv2("%s",row.names=1,header = %s)
478 """ % (self.DictPathOut['Contout'], header, self.DictPathOut['RData'])
482 """ % self.parent.RscriptsPath['Rgraph']
486 make.simi.afc(dm,chistabletot, lim=%i, alpha = %.2f, movie = %s)
487 """ % (simi3d.spin_1.GetValue(), float(simi3d.slider_1.GetValue())/100, movie)
488 tmpfile = tempfile.mktemp(dir=self.parent.TEMPDIR)
489 tmp = open(tmpfile,'w')
494 def dendroandbarplot(table, rownames, colnames, rgraph, tmpgraph, intxt = False, dendro=False) :
496 txttable = 'c(' + ','.join([','.join(line) for line in table]) + ')'
497 rownb = len(rownames)
498 rownames = 'c("' + '","'.join(rownames) + '")'
499 colnames = 'c("' + '","'.join(colnames) + '")'
503 di <- matrix(data=%s, nrow=%i, byrow = TRUE)
506 """ % (txttable, rownb, rownames, colnames)
513 height <- (30*ncol(di)) + (15*nrow(di))
514 height <- ifelse(height <= 400, 400, height)
516 open_file_graph("%s", width=width, height=height)
517 plot.dendro.lex(tree.cut1$tree.cl, di)
518 """ % (ffr(dendro),ffr(rgraph), ffr(tmpgraph))
521 def barplot(table, rownames, colnames, rgraph, tmpgraph, intxt = False) :
523 txttable = 'c(' + ','.join([','.join(line) for line in table]) + ')'
524 #width = 100 + (15 * len(rownames)) + (100 * len(colnames))
525 #height = len(rownames) * 15
526 rownb = len(rownames)
529 rownames = 'c("' + '","'.join(rownames) + '")'
530 colnames = 'c("' + '","'.join(colnames) + '")'
535 di <- matrix(data=%s, nrow=%i, byrow = TRUE)
536 di[is.na(di)] <- max(di, na.rm=TRUE) + 2
539 """ % (txttable, rownb, rownames, colnames)
544 color = rainbow(nrow(di))
545 width <- 100 + (20*length(rownames(di))) + (100 * length(colnames(di)))
546 height <- nrow(di) * 15
547 if (height < 400) { height <- 400}
548 open_file_graph("%s",width = width, height = height)
550 layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(7)))
552 coord <- barplot(as.matrix(di), beside = TRUE, col = color, space = c(0.1,0.6))
557 lcoord <- apply(cc, 1, mean)
560 amp <- abs(max(di) - min(di))
567 d <- signif(amp%%/%%10,1)
572 if ((i/d) == (i%%/%%d)) {
577 plot(0, axes = FALSE, pch = '')
578 legend(x = 'center' , rownames(di), fill = color)
580 """ % (rgraph, ffr(tmpgraph))
583 #def RAfcUci(DictAfcUciOut, nd=2, RscriptsPath='', PARCEX='0.8'):
589 # dataact<-read.csv2("%s")
590 # """ % (DictAfcUciOut['TableCont'])#, encoding)
592 # datasup<-read.csv2("%s")
593 # """ % (DictAfcUciOut['TableSup'])#, encoding)
595 # dataet<-read.csv2("%s")
596 # """ % (DictAfcUciOut['TableEt'])#, encoding)
598 # datatotsup<-cbind(dataact,datasup)
599 # datatotet<-cbind(dataact,dataet)
600 # afcact<-ca(dataact,nd=nd)
601 # afcsup<-ca(datatotsup,supcol=((ncol(dataact)+1):ncol(datatotsup)),nd=nd)
602 # afcet<-ca(datatotet,supcol=((ncol(dataact)+1):ncol(datatotet)),nd=nd)
603 # afctot<-afcsup$colcoord
604 # rownames(afctot)<-afcsup$colnames
605 # colnames(afctot)<-paste('coord. facteur',1:nd,sep=' ')
606 # afctot<-cbind(afctot,mass=afcsup$colmass)
607 # afctot<-cbind(afctot,distance=afcsup$coldist)
608 # afctot<-cbind(afctot,intertie=afcsup$colinertia)
609 # rcolet<-afcet$colsup
610 # afctmp<-afcet$colcoord[rcolet,]
611 # rownames(afctmp)<-afcet$colnames[rcolet]
612 # afctmp<-cbind(afctmp,afcet$colmass[rcolet])
613 # afctmp<-cbind(afctmp,afcet$coldist[rcolet])
614 # afctmp<-cbind(afctmp,afcet$colinertia[rcolet])
615 # afctot<-rbind(afctot,afctmp)
616 # write.csv2(afctot,file = "%s")
618 # """ % (DictAfcUciOut['afc_row'], RscriptsPath['Rgraph'])
624 # PlotAfc(afcet,filename="%s",toplot=c%s, PARCEX=PARCEX)
625 # """ % (DictAfcUciOut['AfcColAct'], "('none','active')")
627 # PlotAfc(afcsup,filename="%s",toplot=c%s, PARCEX=PARCEX)
628 # """ % (DictAfcUciOut['AfcColSup'], "('none','passive')")
629 # txt += """PlotAfc(afcet,filename="%s", toplot=c%s, PARCEX=PARCEX)
630 # """ % (DictAfcUciOut['AfcColEt'], "('none','passive')")
632 # PlotAfc(afcet,filename="%s", toplot=c%s, PARCEX=PARCEX)
633 # """ % (DictAfcUciOut['AfcRow'], "('all','none')")
634 # f = open(DictAfcUciOut['Rafcuci'], 'w')
638 class PrintSimiScript(PrintRScript) :
639 def make_script(self) :
641 self.packages(['igraph', 'proxy', 'Matrix'])
642 self.sources([self.analyse.parent.RscriptsPath['simi'], self.analyse.parent.RscriptsPath['Rgraph']])
647 """ % (self.pathout['mat01.csv'], self.pathout['actives.csv'], self.pathout['selected.csv'])
650 cn <- read.table(cn.path, sep=';', quote='"')
651 colnames(dm) <- cn[,1]
652 sel.col <- read.csv2(selected.col)
653 dm <- dm[, sel.col[,1] + 1]
656 if self.parametres['coeff'] == 0 :
666 if self.parametres['coeff'] == 1 :
670 mat <- simil(dm, method = 'Russel', diag = TRUE, upper = TRUE, by_rows = FALSE)
672 elif self.analyse.indices[self.parametres['coeff']] == 'binomial' :
678 elif self.parametres['coeff'] != 0 :
679 method = self.analyse.indices[self.parametres['coeff']]
682 mat <- simil(dm, method = method, diag = TRUE, upper = TRUE, by_rows = FALSE)
683 """ % self.analyse.indices[self.parametres['coeff']]
685 mat <- as.matrix(stats::as.dist(mat,diag=TRUE,upper=TRUE))
687 mat[is.infinite(mat)] <- 0
689 if self.parametres['layout'] == 0 : layout = 'random'
690 if self.parametres['layout'] == 1 : layout = 'circle'
691 if self.parametres['layout'] == 2 : layout = 'frutch'
692 if self.parametres['layout'] == 3 : layout = 'kawa'
693 if self.parametres['layout'] == 4 : layout = 'graphopt'
696 if self.parametres['type_graph'] == 0 : type = 'tkplot'
697 if self.parametres['type_graph'] == 1 :
700 dirout = os.path.dirname(self.pathout['mat01'])
701 while os.path.exists(os.path.join(dirout,'graph_simi_'+str(graphnb)+'.png')):
703 self.filename = ffr(os.path.join(dirout,'graph_simi_'+str(graphnb)+'.png'))
704 if self.parametres['type_graph'] == 2 : type = 'rgl'
706 if self.parametres['arbremax'] :
708 self.txtgraph += ' - arbre maximum'
709 else : arbremax = 'FALSE'
711 if self.parametres['coeff_tv'] :
712 coeff_tv = self.parametres['coeff_tv_nb']
713 tvminmax = 'c(NULL,NULL)'
714 elif not self.parametres['coeff_tv'] or self.parametres.get('sformchi', False) :
716 tvminmax = 'c(%i, %i)' %(self.parametres['tvmin'], self.parametres['tvmax'])
717 if self.parametres['coeff_te'] : coeff_te = 'c(%i,%i)' % (self.parametres['coeff_temin'], self.parametres['coeff_temax'])
718 else : coeff_te = 'NULL'
720 if self.parametres['vcex'] or self.parametres.get('cexfromchi', False) :
721 vcexminmax = 'c(%i/10,%i/10)' % (self.parametres['vcexmin'],self.parametres['vcexmax'])
723 vcexminmax = 'c(NULL,NULL)'
724 if not self.parametres['label_v'] : label_v = 'FALSE'
725 else : label_v = 'TRUE'
727 if not self.parametres['label_e'] : label_e = 'FALSE'
728 else : label_e = 'TRUE'
730 if self.parametres['seuil_ok'] : seuil = str(self.parametres['seuil'])
731 else : seuil = 'NULL'
733 cols = str(self.parametres['cols']).replace(')',', max=255)')
734 cola = str(self.parametres['cola']).replace(')',',max=255)')
744 """ % self.parametres['cex']
746 if self.parametres['film'] :
749 """ % self.pathout['film']
761 """ % (label_v, label_e)
769 """ % (self.parametres['width'], self.parametres['height'])
770 if self.parametres['keep_coord'] :
772 coords <- try(coords, TRUE)
773 if (!is.matrix(coords)) {
783 """ % self.parametres['alpha']
786 """ % self.parametres['alpha']
787 #############################################
788 if self.parametres.get('bystar',False) :
792 print self.parametres
793 for i,et in enumerate(self.parametres['stars']) :
796 """ % (i+1, ','.join(et[1:]))
799 """ % ("','".join([val[0] for val in self.tableau.etline]))
803 for (i in 1:length(unetoile)) {
806 if (length(tosum) > 1) {
807 fsum <- cbind(fsum, colSums(dm[tosum,]))
809 fsum <- cbind(fsum, dm[tosum,])
813 lex <- AsLexico2(fsum, chip=TRUE)
814 dcol <- apply(lex[[4]],1,which.max)
815 toblack <- apply(lex[[4]],1,max)
816 gcol <- rainbow(length(unetoile))
818 vertex.label.color <- gcol[dcol]
819 vertex.label.color[which(toblack <= 3.84)] <- 'black'
820 leg <- list(unetoile=unetoile, gcol=gcol)
821 cols <- vertex.label.color
822 chivertex.size <- norm.vec(toblack, vcexminmax[1], vcexminmax[2])
824 """ % (self.parent.RscriptsPath['chdfunct'])
827 vertex.label.color <- 'black'
831 #############################################
835 # g.ori <- graph.adjacency(mat, mode='lower', weighted = TRUE)
836 # w.ori <- E(g.ori)$weight
838 # if (method == 'cooc') {
839 # E(g.ori)$weight <- 1 / w.ori
841 # E(g.ori)$weigth <- 1 - w.ori
843 # g.max <- minimum.spanning.tree(g.ori)
844 # if (method == 'cooc') {
845 # E(g.max)$weight <- 1 / E(g.max)$weight
847 # E(g.max)$weight <- 1 - E(g.max)$weight
856 x <- list(mat = mat, eff = eff)
857 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)
858 """ % (method, type, layout, arbremax, coeff_tv, coeff_te)
860 if self.parametres.get('bystar',False) :
861 if self.parametres.get('cexfromchi', False) :
863 label.cex<-chivertex.size
869 if self.parametres.get('sfromchi', False) :
871 vertex.size <- norm.vec(toblack, minmaxeff[1], minmaxeff[2])
882 lchi <- read.table("%s")
885 if 'selected_col' in dir(self.tableau) :
889 if tmpchi and self.parametres.get('cexfromchi', False) :
891 label.cex <- norm.vec(lchi, vcexminmax[1], vcexminmax[2])
895 if (is.null(vcexminmax[1])) {
898 label.cex <- graph.simi$label.cex
901 if tmpchi and self.parametres.get('sfromchi', False) :
903 vertex.size <- norm.vec(lchi, minmaxeff[1], minmaxeff[2])
907 if (is.null(minmaxeff[1])) {
910 vertex.size <- graph.simi$eff
913 txt += """ vertex.size <- NULL """
915 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)
916 save.image(file="%s")
917 """ % (type, self.filename, self.pathout['RData'])
922 class WordCloudRScript(PrintRScript) :
923 def make_script(self) :
924 self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
925 self.packages(['wordcloud'])
926 bg_col = Rcolor(self.parametres['col_bg'])
927 txt_col = Rcolor(self.parametres['col_text'])
929 act <- read.csv2("%s", header = FALSE, row.names=1, sep='\t')
930 selected.col <- read.table("%s")
931 toprint <- as.matrix(act[selected.col[,1] + 1,])
932 rownames(toprint) <- rownames(act)[selected.col[,1] + 1]
934 if (nrow(toprint) > maxword) {
935 toprint <- as.matrix(toprint[order(toprint[,1], decreasing=TRUE),])
936 toprint <- as.matrix(toprint[1:maxword,])
938 open_file_graph("%s", width = %i, height = %i)
940 wordcloud(row.names(toprint), toprint[,1], scale=c(%f,%f), random.order=FALSE, colors=rgb%s)
942 """ % (ffr(self.analyse.pathout['actives_eff.csv']), ffr(self.analyse.pathout['selected.csv']), self.parametres['maxword'], ffr(self.parametres['graphout']), self.parametres['width'], self.parametres['height'], bg_col, self.parametres['maxcex'], self.parametres['mincex'], txt_col)