+class PrintSimiScript(PrintRScript) :
+ def make_script(self) :
+ self.txtgraph = ''
+ self.packages(['igraph', 'proxy', 'Matrix'])
+ self.sources([self.analyse.parent.RscriptsPath['simi'], self.analyse.parent.RscriptsPath['Rgraph']])
+ txt = ''
+ if not self.parametres['keep_coord'] and not (self.parametres['type'] == 'simimatrix' or self.parametres['type'] == 'simiclustermatrix') :
+ txt += """
+ dm.path <- "%s"
+ cn.path <- "%s"
+ selected.col <- "%s"
+ """ % (ffr(self.pathout['mat01.csv']), ffr(self.pathout['actives.csv']), ffr(self.pathout['selected.csv']))
+ if 'word' in self.parametres :
+ txt += """
+ word <- TRUE
+ index <- %i + 1
+ """ % self.parametres['word']
+ else :
+ txt += """
+ word <- FALSE
+ index <- NULL
+ """
+ txt += """
+ dm <-readMM(dm.path)
+ cn <- read.table(cn.path, sep="\t", quote='"')
+ colnames(dm) <- cn[,1]
+ if (file.exists(selected.col)) {
+ sel.col <- read.csv2(selected.col, header = FALSE)
+ sel.col <- sel.col[,1] + 1
+ } else {
+ sel.col <- 1:ncol(dm)
+ }
+ if (!word) {
+ dm <- dm[, sel.col]
+ } else {
+ forme <- colnames(dm)[index]
+ if (!index %in% sel.col) {
+ sel.col <- append(sel.col, index)
+ }
+ dm <- dm[, sel.col]
+ index <- which(colnames(dm) == forme)
+ }
+ """
+ elif not self.parametres['keep_coord'] and (self.parametres['type'] == 'simimatrix' or self.parametres['type'] == 'simiclustermatrix'):
+ txt += """
+ dm.path <- "%s"
+ selected.col <- "%s"
+ """ % (ffr(self.pathout['mat01.csv']), ffr(self.pathout['selected.csv']))
+ if 'word' in self.parametres :
+ txt += """
+ word <- TRUE
+ index <- %i + 1
+ """ % self.parametres['word']
+ else :
+ txt += """
+ word <- FALSE
+ """
+ txt += """
+ dm <-read.csv2(dm.path)
+ dm <- as.matrix(dm)
+ if (file.exists(selected.col)) {
+ sel.col <- read.csv2(selected.col, header = FALSE)
+ sel.col <- sel.col[,1] + 1
+ } else {
+ sel.col <- 1:ncol(dm)
+ }
+ if (!word) {
+ dm <- dm[, sel.col]
+ } else {
+ forme <- colnames(dm)[index]
+ if (!index %in% sel.col) {
+ sel.col <- append(sel.col, index)
+ }
+ dm <- dm[, sel.col]
+ index <- which(colnames(dm) == forme)
+ }
+ """
+ else :
+ txt += """
+ load("%s")
+ """ % ffr(self.pathout['RData.RData'])
+
+ if self.parametres['coeff'] == 0 :
+ method = 'cooc'
+ if not self.parametres['keep_coord'] :
+ txt += """
+ method <- 'cooc'
+ mat <- make.a(dm)
+ """
+ elif self.analyse.indices[self.parametres['coeff']] == 'Jaccard' :
+ method = 'Jaccard'
+ if not self.parametres['keep_coord'] :
+ txt += """
+ method <- 'Jaccard'
+ mat <- sparse.jaccard(dm)
+ """
+ else :
+ if not self.parametres['keep_coord'] :
+ txt += """
+ dm <- as.matrix(dm)
+ """
+ if self.parametres['coeff'] == 1 :
+ method = 'prcooc'
+ txt += """
+ method <- 'Russel'
+ mat <- simil(dm, method = 'Russel', diag = TRUE, upper = TRUE, by_rows = FALSE)
+ """
+ elif self.analyse.indices[self.parametres['coeff']] == 'binomial' :
+ method = 'binomial'
+ if not self.parametres['keep_coord'] :
+ txt += """
+ method <- 'binomial'
+ mat <- binom.sim(dm)
+ """
+ elif self.parametres['coeff'] != 0 and self.analyse.indices[self.parametres['coeff']] != 'Jaccard':
+ method = self.analyse.indices[self.parametres['coeff']]
+ if not self.parametres['keep_coord'] :
+ txt += """
+ method <-"%s"
+ mat <- simil(dm, method = method, diag = TRUE, upper = TRUE, by_rows = FALSE)
+ """ % self.analyse.indices[self.parametres['coeff']]
+ if not self.parametres['keep_coord'] :
+ txt += """
+ mat <- as.matrix(stats::as.dist(mat,diag=TRUE,upper=TRUE))
+ mat[is.na(mat)] <- 0
+ if (length(which(mat == Inf))) {
+ infp <- which(mat == Inf)
+ mat[infp] <- NA
+ maxmat <- max(mat, na.rm = TRUE)
+ if (maxmat > 0) {
+ maxmat <- maxmat + 1
+ } else {
+ maxmat <- 0
+ }
+ mat[infp] <- maxmat
+ }
+ if (length(which(mat == -Inf))) {
+ infm <- which(mat == -Inf)
+ mat[infm] <- NA
+ minmat <- min(mat, na.rm = TRUE)
+ if (maxmat < 0) {
+ minmat <- minmat - 1
+ } else {
+ minmat <- 0
+ }
+ mat[infm] <- minmat
+ }
+ """
+ if 'word' in self.parametres and not self.parametres['keep_coord'] :
+ txt += """
+ mat <- graph.word(mat, index)
+ cs <- colSums(mat)
+ if (length(which(cs==0))) mat <- mat[,-which(cs==0)]
+ rs <- rowSums(mat)
+ if (length(which(rs==0))) mat <- mat[-which(rs==0),]
+ if (length(which(cs==0))) dm <- dm[,-which(cs==0)]
+ if (word) {
+ index <- which(colnames(mat)==forme)
+ }
+ """
+
+ if self.parametres['layout'] == 0 : layout = 'random'
+ if self.parametres['layout'] == 1 : layout = 'circle'
+ if self.parametres['layout'] == 2 : layout = 'frutch'
+ if self.parametres['layout'] == 3 : layout = 'kawa'
+ if self.parametres['layout'] == 4 : layout = 'graphopt'
+ if self.parametres['layout'] == 5 : layout = 'spirale'
+ if self.parametres['layout'] == 6 : layout = 'spirale3D'
+
+
+ self.filename=''
+ if self.parametres['type_graph'] == 0 : type = 'tkplot'
+ if self.parametres['type_graph'] == 1 :
+ graphnb = 1
+ type = 'nplot'
+ dirout = os.path.dirname(self.pathout['mat01.csv'])
+ while os.path.exists(os.path.join(dirout,'graph_simi_'+str(graphnb)+'.png')):
+ graphnb +=1
+ self.filename = ffr(os.path.join(dirout,'graph_simi_'+str(graphnb)+'.png'))
+ if self.parametres['type_graph'] == 2 : type = 'rgl'
+ if self.parametres['type_graph'] == 3 :
+ graphnb = 1
+ type = 'web'
+ dirout = os.path.dirname(self.pathout['mat01.csv'])
+ while os.path.exists(os.path.join(dirout,'web_'+str(graphnb))):
+ graphnb +=1
+ self.filename = ffr(os.path.join(dirout,'web_'+str(graphnb)))
+ os.mkdir(self.filename)
+ self.filename = os.path.join(self.filename, 'gexf.gexf')
+ if self.parametres['type_graph'] == 4 :
+ graphnb = 1
+ type = 'rglweb'
+ dirout = os.path.dirname(self.pathout['mat01.csv'])
+ while os.path.exists(os.path.join(dirout,'webrgl_'+str(graphnb))):
+ graphnb +=1
+ self.filename = ffr(os.path.join(dirout,'webrgl_'+str(graphnb)))
+ os.mkdir(self.filename)
+
+ if self.parametres['arbremax'] :
+ arbremax = 'TRUE'
+ self.txtgraph += ' - arbre maximum'
+ else : arbremax = 'FALSE'
+
+ if self.parametres['coeff_tv'] :
+ coeff_tv = self.parametres['coeff_tv_nb']
+ tvminmax = 'c(NULL,NULL)'
+ elif not self.parametres['coeff_tv'] or self.parametres.get('sformchi', False) :
+ coeff_tv = 'NULL'
+ tvminmax = 'c(%i, %i)' %(self.parametres['tvmin'], self.parametres['tvmax'])
+ if self.parametres['coeff_te'] : coeff_te = 'c(%i,%i)' % (self.parametres['coeff_temin'], self.parametres['coeff_temax'])
+ else : coeff_te = 'NULL'
+
+ if self.parametres['vcex'] or self.parametres.get('cexfromchi', False) :
+ vcexminmax = 'c(%i/10,%i/10)' % (self.parametres['vcexmin'],self.parametres['vcexmax'])
+ else :
+ vcexminmax = 'c(NULL,NULL)'
+ if not self.parametres['label_v'] : label_v = 'FALSE'
+ else : label_v = 'TRUE'
+
+ if not self.parametres['label_e'] : label_e = 'FALSE'
+ else : label_e = 'TRUE'
+
+ if self.parametres['seuil_ok'] : seuil = str(self.parametres['seuil'])
+ else : seuil = 'NULL'
+
+ if not self.parametres.get('edgecurved', False) :
+ ec = 'FALSE'
+ else :
+ ec = 'TRUE'
+
+ txt += """
+ edge.curved <- %s
+ """ % ec
+
+ cols = str(self.parametres['cols']).replace(')',', max=255)')
+ cola = str(self.parametres['cola']).replace(')',',max=255)')
+
+ txt += """
+ minmaxeff <- %s
+ """ % tvminmax
+ txt += """
+ vcexminmax <- %s
+ """ % vcexminmax
+ txt += """
+ cex = %i/10
+ """ % self.parametres['cex']
+
+ if self.parametres['film'] :
+ txt += """
+ film <- "%s"
+ """ % ffr(self.pathout['film'])
+ else :
+ txt += """
+ film <- NULL
+ """
+ txt += """
+ seuil <- %s
+ if (!is.null(seuil)) {
+ if (method!='cooc') {
+ seuil <- seuil/1000
+ }
+ }
+ """ % seuil
+
+ txt += """
+ label.v <- %s
+ label.e <- %s
+ """ % (label_v, label_e)
+ txt += """
+ cols <- rgb%s
+ cola <- rgb%s
+ """ % (cols, cola)
+ txt += """
+ width <- %i
+ height <- %i
+ """ % (self.parametres['width'], self.parametres['height'])
+ if self.parametres['keep_coord'] :
+ txt += """
+ coords <- try(coords, TRUE)
+ if (!is.matrix(coords)) {
+ coords<-NULL
+ }
+ """
+ else :
+ txt += """
+ coords <- NULL
+ """
+ txt += """
+ alpha <- %i/100
+ """ % self.parametres['alpha']
+ txt += """
+ alpha <- %i/100
+ """ % self.parametres['alpha']
+#############################################
+ if self.parametres.get('bystar',False) :
+ txt += """
+ et <- list()
+ """
+ for i, line in enumerate(self.parametres['listet']) :
+ txt+= """
+ et[[%i]] <- c(%s)
+ """ % (i+1, ','.join([`val + 1` for val in line]))
+ txt+= """
+ unetoile <- c('%s')
+ """ % ("','".join([val for val in self.parametres['selectedstars']]))
+ txt += """
+ fsum <- NULL
+ rs <- rowSums(dm)
+ for (i in 1:length(unetoile)) {
+ print(unetoile[i])
+ tosum <- et[[i]]
+ if (length(tosum) > 1) {
+ fsum <- cbind(fsum, colSums(dm[tosum,]))
+ } else {
+ fsum <- cbind(fsum, dm[tosum,])
+ }
+ }
+ source("%s")
+ lex <- AsLexico2(fsum, chip=TRUE)
+ dcol <- apply(lex[[4]],1,which.max)
+ toblack <- apply(lex[[4]],1,max)
+ gcol <- rainbow(length(unetoile))
+ #gcol[2] <- 'orange'
+ vertex.label.color <- gcol[dcol]
+ vertex.label.color[which(toblack <= 3.84)] <- 'black'
+ leg <- list(unetoile=unetoile, gcol=gcol)
+ cols <- vertex.label.color
+ chivertex.size <- norm.vec(toblack, vcexminmax[1], vcexminmax[2])
+
+ """ % (ffr(self.analyse.parent.RscriptsPath['chdfunct']))
+ else :
+ txt += """
+ vertex.label.color <- 'black'
+ chivertex.size <- 1
+ leg<-NULL
+ """
+#############################################
+
+# txt += """
+# eff <- colSums(dm)
+# g.ori <- graph.adjacency(mat, mode='lower', weighted = TRUE)
+# w.ori <- E(g.ori)$weight
+# if (max.tree) {
+# if (method == 'cooc') {
+# E(g.ori)$weight <- 1 / w.ori
+# } else {
+# E(g.ori)$weigth <- 1 - w.ori
+# }
+# g.max <- minimum.spanning.tree(g.ori)
+# if (method == 'cooc') {
+# E(g.max)$weight <- 1 / E(g.max)$weight
+# } else {
+# E(g.max)$weight <- 1 - E(g.max)$weight
+# }
+# g.toplot <- g.max
+# } else {
+# g.toplot <- g.ori
+# }
+# """
+ if self.parametres['com'] :
+ com = `self.parametres['communities']`
+ else :
+ com = 'NULL'
+ if self.parametres['halo'] :
+ halo = 'TRUE'
+ else :
+ halo = 'FALSE'
+ txt += """
+ communities <- %s
+ halo <- %s
+ """ % (com, halo)
+ txt += """
+ eff <- colSums(dm)
+ x <- list(mat = mat, eff = eff)
+ graph.simi <- do.simi(x, method='%s', seuil = seuil, p.type = '%s', layout.type = '%s', max.tree = %s, coeff.vertex=%s, coeff.edge = %s, minmaxeff = minmaxeff, vcexminmax = vcexminmax, cex = cex, coords = coords, communities = communities, halo = halo, index.word=index)
+ """ % (method, type, layout, arbremax, coeff_tv, coeff_te)
+
+ if self.parametres.get('bystar',False) :
+ if self.parametres.get('cexfromchi', False) :
+ txt+="""
+ label.cex<-chivertex.size
+ """
+ else :
+ txt+="""
+ label.cex <- cex
+ """
+ if self.parametres.get('sfromchi', False) :
+ txt += """
+ vertex.size <- norm.vec(toblack, minmaxeff[1], minmaxeff[2])
+ """
+ else :
+ txt += """
+ vertex.size <- NULL
+ """
+ else :
+ #print self.parametres
+ if (self.parametres['type'] == 'clustersimitxt' and self.parametres.get('tmpchi', False)) or (self.parametres['type'] in ['simimatrix','simiclustermatrix'] and 'tmpchi' in self.parametres):
+ txt += """
+ lchi <- read.table("%s")
+ lchi <- lchi[,1]
+ """ % ffr(self.parametres['tmpchi'])
+ txt += """
+ lchi <- lchi[sel.col]
+ """
+ if self.parametres['type'] in ['clustersimitxt', 'simimatrix', 'simiclustermatrix'] and self.parametres.get('cexfromchi', False) :
+ txt += """
+ label.cex <- norm.vec(lchi, vcexminmax[1], vcexminmax[2])
+ """
+ else :
+ txt += """
+ if (is.null(vcexminmax[1])) {
+ label.cex <- cex
+ } else {
+ label.cex <- graph.simi$label.cex
+ }
+ """
+ if (self.parametres['type'] in ['clustersimitxt', 'simimatrix', 'simiclustermatrix']) and self.parametres.get('sfromchi', False):
+ txt += """
+ vertex.size <- norm.vec(lchi, minmaxeff[1], minmaxeff[2])
+ if (!length(vertex.size)) vertex.size <- 0
+ """
+ else :
+ txt += """
+ if (is.null(minmaxeff[1])) {
+ vertex.size <- 0
+ } else {
+ vertex.size <- graph.simi$eff
+ }
+ """
+ #txt += """ vertex.size <- NULL """
+ if self.parametres['svg'] : svg = 'TRUE'
+ else : svg = 'FALSE'
+ txt += """
+ svg <- %s
+ """ % svg
+ txt += """
+ vertex.col <- cols
+ col.from.proto <- F
+ if (col.from.proto) {
+ proto.col <- read.table('/tmp/matcol.csv')
+ v.proto.names <- make.names(proto.col[,1])
+ v.proto.col <- as.character(proto.col[,2])
+ v.proto.col[which(v.proto.col=='black')] <- 'yellow'
+ v.names <- V(graph.simi$graph)$name
+ num.color <- sapply(v.names, function(x) {if (x %%in%% v.proto.names) {v.proto.col[which(v.proto.names==x)]} else {'pink'}})
+ vertex.col <- num.color
+ V(graph.simi$graph)$proto.color <- vertex.col
+ }
+ if (!is.null(graph.simi$com)) {
+ com <- graph.simi$com
+ colm <- rainbow(length(com))
+ if (vertex.size != 0 || graph.simi$halo) {
+ vertex.label.color <- 'black'
+ vertex.col <- colm[membership(com)]
+ } else {
+ vertex.label.color <- colm[membership(com)]
+ }
+ }
+ if (!length(graph.simi$elim)==0) {
+ vertex.label.color <- vertex.label.color[-graph.simi$elim]
+ if (length(label.cex > 1)) {
+ label.cex <- label.cex[-graph.simi$elim]
+ }
+ }
+ coords <- plot.simi(graph.simi, p.type='%s',filename="%s", vertex.label = label.v, edge.label = label.e, vertex.col = vertex.col, 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, edge.curved = edge.curved, svg = svg)
+ save.image(file="%s")
+ """ % (type, self.filename, ffr(self.pathout['RData']))
+
+ self.add(txt)
+ self.write()
+
+class WordCloudRScript(PrintRScript) :
+ def make_script(self) :
+ self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
+ self.packages(['wordcloud'])
+ bg_col = Rcolor(self.parametres['col_bg'])
+ txt_col = Rcolor(self.parametres['col_text'])
+ if self.parametres['svg'] :
+ svg = 'TRUE'
+ else :
+ svg = 'FALSE'
+ txt = """
+ svg <- %s
+ """ % svg
+ txt += """
+ act <- read.csv2("%s", header = FALSE, row.names=1, sep='\t')
+ selected.col <- read.table("%s")
+ toprint <- as.matrix(act[selected.col[,1] + 1,])
+ rownames(toprint) <- rownames(act)[selected.col[,1] + 1]
+ maxword <- %i
+ if (nrow(toprint) > maxword) {
+ toprint <- as.matrix(toprint[order(toprint[,1], decreasing=TRUE),])
+ toprint <- as.matrix(toprint[1:maxword,])
+ }
+ open_file_graph("%s", width = %i, height = %i , svg = svg)
+ par(bg=rgb%s)
+ wordcloud(row.names(toprint), toprint[,1], scale=c(%f,%f), random.order=FALSE, colors=rgb%s)
+ dev.off()
+ """ % (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)
+ self.add(txt)
+ self.write()
+
+class ProtoScript(PrintRScript) :
+ def make_script(self) :
+ self.sources([self.analyse.parent.RscriptsPath['Rgraph'], self.analyse.parent.RscriptsPath['prototypical.R']])
+ self.packages(['wordcloud'])
+ if self.parametres.get('cloud', False) :
+ cloud = 'TRUE'
+ else :
+ cloud = 'FALSE'
+ txt = """
+ errorn <- function(x) {
+ qnorm(0.975)*sd(x)/sqrt(lenght(n))
+ }
+ errort <- function(x) {
+ qt(0.975,df=lenght(x)-1)*sd(x)/sqrt(lenght(x))
+ }
+ mat <- read.csv2("%s", header = FALSE, row.names=1, sep='\t', quote='"', dec='.')
+ open_file_graph("%s",height=800, width=1000)
+ prototypical(mat, mfreq = %s, mrank = %s, cloud = FALSE, cexrange=c(1,2.4), cexalpha= c(0.4, 1), type = '%s', mat.col.path='/tmp/matcol.csv')
+ dev.off()
+ """ % (ffr(self.analyse.pathout['table.csv']), ffr(self.analyse.pathout['proto.png']), self.parametres['limfreq'], self.parametres['limrang'], self.parametres['typegraph'])
+ self.add(txt)
+ self.write()
+
+
+class ExportAfc(PrintRScript) :
+ def make_script(self) :
+ self.source([self.analyse.parent.RscriptsPath['Rgraph']])
+ self.packages(['rgexf'])
+ txt = """
+ """
+
+class MergeGraphes(PrintRScript) :
+ def __init__(self, analyse):
+ self.script = u"#Script genere par IRaMuTeQ - %s\n" % datetime.now().ctime()
+ self.pathout = PathOut()
+ self.parametres = analyse.parametres
+ self.scriptout = self.pathout['temp']
+ self.analyse = analyse
+
+ def make_script(self) :
+ #FIXME
+
+ txt = """
+ library(igraph)
+ library(Matrix)
+ graphs <- list()
+ """
+ load = """
+ load("%s")
+ g <- graph.simi$graph
+ V(g)$weight <- (graph.simi$mat.eff/nrow(dm))*100
+ graphs[['%s']] <- g
+ """
+ for i, graph in enumerate(self.parametres['graphs']) :
+ path = os.path.dirname(graph)
+ gname = ''.join(['g', `i`])
+ RData = os.path.join(path,'RData.RData')
+ txt += load % (ffr(RData), gname)
+ self.add(txt)
+ self.sources([self.analyse.parent.RscriptsPath['simi']])
+ txt = """
+ merge.type <- 'proto'
+ if (merge.type == 'normal') {
+ ng <- merge.graph(graphs)
+ } else {
+ ng <- merge.graph.proto(graphs)
+ }
+ ngraph <- list(graph=ng, layout=layout.fruchterman.reingold(ng, dim=3), labex.cex=V(ng)$weight)
+ write.graph(ng, "%s", format = 'graphml')
+ """ % ffr(self.parametres['grapheout'])
+ self.add(txt)
+
+class TgenSpecScript(PrintRScript):
+ def make_script(self):
+ self.packages(['textometry'])
+ txt = """
+ tgen <- read.csv2("%s", row.names = 1, sep = '\\t')
+ """ % ffr(self.parametres['tgeneff'])
+ txt += """
+ tot <- tgen[nrow(tgen), ]
+ result <- NULL
+ tgen <- tgen[-nrow(tgen),]
+ for (i in 1:nrow(tgen)) {
+ mat <- rbind(tgen[i,], tot - tgen[i,])
+ specmat <- specificities(mat)
+ result <- rbind(result, specmat[1,])
+ }
+ colnames(result) <- colnames(tgen)
+ row.names(result) <- rownames(tgen)
+ write.table(result, file = "%s", sep='\\t', col.names = NA)
+ """ % ffr(self.pathout['tgenspec.csv'])
+ self.add(txt)
+
+class TgenProfScript(PrintRScript):
+ def make_script(self):
+ self.sources([self.analyse.ira.RscriptsPath['chdfunct']])
+ txt = """
+ tgen <- read.csv2("%s", row.names = 1, sep = '\\t')
+ """ % ffr(self.parametres['tgeneff'])
+ txt += """
+ tgenlem <- read.csv2("%s", row.names = 1, sep = '\\t')
+ """ % ffr(self.parametres['tgenlemeff'])
+ txt += """
+ res <- build.prof.tgen(tgen)
+ write.table(res$chi2, file = "%s", sep='\\t', col.names = NA)
+ write.table(res$pchi2, file = "%s", sep='\\t', col.names = NA)
+ """ % (ffr(self.pathout['tgenchi2.csv']), ffr(self.pathout['tgenpchi2.csv']))
+ txt += """
+ reslem <- build.prof.tgen(tgenlem)
+ write.table(reslem$chi2, file = "%s", sep='\\t', col.names = NA)
+ write.table(reslem$pchi2, file = "%s", sep='\\t', col.names = NA)
+ """ % (ffr(self.pathout['tgenlemchi2.csv']), ffr(self.pathout['tgenlempchi2.csv']))
+ self.add(txt)
+
+class FreqMultiScript(PrintRScript):
+ def make_script(self):
+ self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
+ txt = """
+ freq <- read.csv2("%s", row.names=1, sep='\\t', dec='.')
+ """ % ffr(self.pathout['frequences.csv'])
+ txt += """
+ toplot <- freq[order(freq[,2]) ,2]
+ toplot.names = rownames(freq)[order(freq[,2])]
+ h <- 80 + (20 * nrow(freq))
+ open_file_graph("%s",height=h, width=500)
+ par(mar=c(3,20,3,3))
+ barplot(toplot, names = toplot.names, horiz=TRUE, las =1, col = rainbow(nrow(freq)))
+ dev.off()
+ """ % ffr(self.pathout['barplotfreq.png'])
+ txt += """
+ toplot <- freq[order(freq[,4]) ,4]
+ toplot.names = rownames(freq)[order(freq[,4])]
+ open_file_graph("%s",height=h, width=500)
+ par(mar=c(3,20,3,3))
+ barplot(toplot, names = toplot.names, horiz=TRUE, las =1, col = rainbow(nrow(freq)))
+ dev.off()
+ """ % ffr(self.pathout['barplotrow.png'])
+ self.add(txt)
+ self.write()
+
+class LabbeScript(PrintRScript) :
+ def make_script(self) :
+ self.sources([self.analyse.parent.RscriptsPath['distance-labbe.R'],
+ self.analyse.parent.RscriptsPath['Rgraph']])
+ txt = """
+ tab <- read.csv2("%s", header=TRUE, sep=';', row.names=1)
+ """ % (ffr(self.pathout['tableafcm.csv']))
+ txt += """
+ dist.mat <- dist.labbe(tab)
+ dist.mat <- as.dist(dist.mat, upper=F, diag=F)
+ write.table(as.matrix(dist.mat), "%s", sep='\t')
+ library(cluster)
+ library(ape)
+ chd <- hclust(dist.mat, method="ward.D2")
+ open_file_graph("%s", width=1000, height=1000, svg=F)
+ par(cex=1.2)
+ plot.phylo(as.phylo(chd), type='unrooted', lab4ut="axial")
+ dev.off()
+ """ % (ffr(self.pathout['distmat.csv']), ffr(self.pathout['labbe-tree.png']))
+ txt +="""
+ open_file_graph("%s", width=1000, height=1000, svg=F)
+ par(mar=c(10,1,1,10))
+ heatmap(as.matrix(dist.mat), symm = T, distfun=function(x) as.dist(x), margins=c(10,10))
+ dev.off()
+ """ % ffr(self.pathout['labbe-heatmap.png'])
+ txt += """
+ #http://stackoverflow.com/questions/3081066/what-techniques-exists-in-r-to-visualize-a-distance-matrix
+ dst <- data.matrix(dist.mat)
+ dim <- ncol(dst)
+ rn <- row.names(as.matrix(dist.mat))
+ open_file_graph("%s", width=1500, height=1000, svg=F)
+ par(mar=c(10,10,3,3))
+ image(1:dim, 1:dim, dst, axes = FALSE, xlab="", ylab="", col=heat.colors(99), breaks=seq(0.01,1,0.01))
+ axis(1, 1:dim, rn, cex.axis = 0.9, las=3)
+ axis(2, 1:dim, rn, cex.axis = 0.9, las=1)
+ text(expand.grid(1:dim, 1:dim), sprintf("%%0.2f", dst), cex=0.6)
+ dev.off()
+ """ % ffr(self.pathout['labbe-matrix.png'])
+ txt += """
+ library(igraph)
+ g <- graph.adjacency(as.matrix(1-dist.mat), mode="lower", weighted=T)
+ write.graph(g, file="%s", format='graphml')
+ open_file_graph("%s", width=1000, height=1000, svg=F)
+ plot(g)
+ dev.off()
+ E(g)$weight <- 1 - E(g)$weight
+ g <- minimum.spanning.tree(g)
+ E(g)$weight <- 1 - E(g)$weight
+ write.graph(g, file="%s", format='graphml')
+ open_file_graph("%s", width=1000, height=1000, svg=F)
+ plot(g)
+ dev.off()
+ """ % (ffr(self.pathout['graph_tot.graphml']), ffr(self.pathout['graph_tot.png']), ffr(self.pathout['graph_min.graphml']), ffr(self.pathout['graph_min.png']))
+ self.add(txt)
+ self.write()
+
+class ChronoChi2Script(PrintRScript) :
+ def make_script(self) :
+ self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
+ print self.parametres
+ txt = """
+ inRData <- "%s"
+ dendrof <- "%s"
+ load(inRData)
+ load(dendrof)
+ """ % (ffr(self.pathout['RData.RData']), ffr(self.pathout['dendrogramme.RData']))
+ txt += """
+ svg <- %s
+ """ % self.parametres['svg']
+ txt += """
+ tc <- which(grepl("%s",rownames(chistabletot)))
+ rn <- rownames(chistabletot)[tc]
+ tc <- tc[order(rn)]
+ dpt <- chistabletot[tc,]
+ tot <- afctable[tc,]
+ tcp <- rowSums(tot)
+ ptc <- tcp/sum(tcp)
+ dpt <- t(dpt)
+ dd <- dpt
+ """ % self.parametres['var'].replace(u'*', u"\\\\*")
+ txt += """
+ classes <- n1[,ncol(n1)]
+ tcl <- table(classes)
+ if ('0' %in% names(tcl)) {
+ to.vire <- which(names(tcl) == '0')
+ tcl <- tcl[-to.vire]
+ }
+ tclp <- tcl/sum(tcl)
+
+ #chi2 colors
+ library(ape)
+ k <- 1e-02
+ lcol <- NULL
+ lk <- k
+ for (i in 1:5) {
+ lcol <- c(lcol, qchisq(1-k,1))
+ k <- k/10
+ lk <- c(lk,k)
+ }
+ lcol <- c(3.84, lcol)
+ lcol <- c(-Inf,lcol)
+ lcol <- c(lcol, Inf)
+ lk <- c(0.05,lk)
+ breaks <- lcol
+ alphas <- seq(0,1, length.out=length(breaks))
+ clod <- rev(as.numeric(tree.cut1$tree.cl$tip.label))
+ #end
+ """
+ txt += """
+ open_file_graph("%s", w=%i, h=%i, svg=svg)
+ """ % (ffr(self.parametres['tmpgraph']), self.parametres['width'], self.parametres['height'])
+ txt += """
+ par(mar=c(3,3,3,3))
+ mat.graphic <- matrix(c(rep(1,nrow(dd)),c(2:(nrow(dd)+1))), ncol=2)
+ mat.graphic <- rbind(mat.graphic, c(max(mat.graphic) + 1 , max(mat.graphic) + 2))
+ hauteur <- tclp[clod] * 0.9
+ heights.graphic <- append(hauteur, 0.1)
+ layout(mat.graphic, heights=heights.graphic, widths=c(0.15,0.85))
+ par(mar=c(0,0,0,0))
+ tree.toplot <- tree.cut1$tree.cl
+ num.label <- as.numeric(tree.cut1$tree.cl$tip.label)
+ col.tree <- rainbow(length(num.label))[num.label]
+ #tree.toplot$tip.label <- paste('classe ', tree.toplot$tip.label)
+ plot.phylo(tree.toplot,label.offset=0.1, cex=1.1, no.margin=T, tip.color = col.tree)
+ for (i in clod) {
+ print(i)
+ par(mar=c(0,0,0,0))
+ lcol <- cut(dd[i,], breaks, include.lowest=TRUE)
+ ulcol <- names(table(lcol))
+ lcol <- as.character(lcol)
+ for (j in 1:length(ulcol)) {
+ lcol[which(lcol==ulcol[j])] <- j
+ }
+ lcol <- as.numeric(lcol)
+ mcol <- rainbow(nrow(dd))[i]
+ last.col <- NULL
+ for (k in alphas) {
+ last.col <- c(last.col, rgb(r=col2rgb(mcol)[1]/255, g=col2rgb(mcol)[2]/255, b=col2rgb(mcol)[3]/255, a=k))
+ }
+ #print(last.col)
+
+ barplot(rep(1,ncol(dd)), width=ptc, names.arg=FALSE, axes=FALSE, col=last.col[lcol], border=rgb(r=0, g=0, b=0, a=0.3))
+ }
+ plot(0,type='n',axes=FALSE,ann=FALSE)
+ label.coords <- barplot(rep(1, ncol(dd)), width=ptc, names.arg = F, las=2, axes=F, ylim=c(0,1), plot=T, col='white')
+ text(x=label.coords, y=0.5, labels=rn[order(rn)], srt=90)
+ dev.off()
+ """
+ self.add(txt)
+ self.write()
+
+class ChronoPropScript(PrintRScript) :
+ def make_script(self) :
+ self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
+ print self.parametres
+ txt = """
+ inRData <- "%s"
+ dendrof <- "%s"
+ load(inRData)
+ load(dendrof)
+ """ % (ffr(self.pathout['RData.RData']), ffr(self.pathout['dendrogramme.RData']))
+ txt += """
+ svg <- %s
+ """ % self.parametres['svg']
+ txt += """
+ tc <- which(grepl("%s",rownames(chistabletot)))
+ rn <- rownames(chistabletot)[tc]
+ tc <- tc[order(rn)]
+ dpt <- chistabletot[tc,]
+ tot <- afctable[tc,]
+ tcp <- rowSums(tot)
+ ptc <- tcp/sum(tcp)
+ dpt <- t(dpt)
+ dd <- dpt
+ """ % self.parametres['var'].replace(u'*', u"\\\\*")
+ txt += """
+ classes <- n1[,ncol(n1)]
+ tcl <- table(classes)
+ if ('0' %in% names(tcl)) {
+ to.vire <- which(names(tcl) == '0')
+ tcl <- tcl[-to.vire]
+ }
+ tclp <- tcl/sum(tcl)
+ """
+ txt += """
+ open_file_graph("%s", w=%i, h=%i, svg=svg)
+ """ % (ffr(self.parametres['tmpgraph']), self.parametres['width'], self.parametres['height'])
+ txt+= """
+ ptt <- prop.table(as.matrix(tot), 1)
+ par(mar=c(10,2,2,2))
+ barplot(t(ptt)[as.numeric(tree.cut1$tree.cl$tip.label),], col=rainbow(ncol(ptt))[as.numeric(tree.cut1$tree.cl$tip.label)], width=ptc, las=3, space=0.05, cex.axis=0.7, border=NA)
+ dev.off()
+ """
+ self.add(txt)
+ self.write()
+
+class ChronoggScript(PrintRScript) :
+ def make_script(self) :
+ self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
+ print self.parametres
+ txt = """
+ library(ggplot2)
+ inRData <- "%s"
+ dendrof <- "%s"
+ load(inRData)
+ load(dendrof)
+ """ % (ffr(self.pathout['RData.RData']), ffr(self.pathout['dendrogramme.RData']))
+ txt += """
+ svg <- %s
+ """ % self.parametres['svg']
+ txt += """
+ tc <- which(grepl("%s",rownames(chistabletot)))
+ rn <- rownames(chistabletot)[tc]
+ tc <- tc[order(rn)]
+ dpt <- chistabletot[tc,]
+ tot <- afctable[tc,]
+ tcp <- rowSums(tot)
+ ptc <- tcp/sum(tcp)
+ dpt <- t(dpt)
+ dd <- dpt
+ """ % self.parametres['var'].replace(u'*', u"\\\\*")
+ txt += """
+ classes <- n1[,ncol(n1)]
+ tcl <- table(classes)
+ if ('0' %in% names(tcl)) {
+ to.vire <- which(names(tcl) == '0')
+ tcl <- tcl[-to.vire]
+ }
+ tclp <- tcl/sum(tcl)
+ ptt <- prop.table(as.matrix(tot), 1)
+ ptt <- ptt[,as.numeric(tree.cut1$tree.cl$tip.label)]
+ rownames(ptt) <- cumsum(ptc)
+ nptt<-as.data.frame(as.table(ptt))
+ nptt[,1]<-as.numeric(as.character(nptt[,1]))
+ col <- rainbow(ncol(ptt))[as.numeric(tree.cut1$tree.cl$tip.label)]
+ """
+ txt += """
+ open_file_graph("%s", w=%i, h=%i, svg=svg)
+ """ % (ffr(self.parametres['tmpgraph']), self.parametres['width'], self.parametres['height'])
+ txt+= """
+ par(mar=c(10,2,2,2))
+ gg <- ggplot(data=nptt, aes(x=Var1,y=Freq,fill=Var2)) + geom_area(alpha=1 , size=0.5, colour="black")
+ gg + scale_fill_manual(values=col)
+ dev.off()
+ """
+ self.add(txt)
+ self.write()
+
+class DendroScript(PrintRScript) :
+ def make_script(self) :
+ if self.parametres['svg'] :
+ typefile = '.svg'
+ else :
+ typefile = '.png'
+ fileout = self.parametres['fileout']
+ width = self.parametres['width']
+ height = self.parametres['height']
+ type_dendro = self.parametres['dendro_type']
+ if self.parametres['taille_classe'] :
+ tclasse = 'TRUE'
+ else :
+ tclasse = 'FALSE'
+ if self.parametres['color_nb'] == 0 :
+ bw = 'FALSE'
+ else :
+ bw = 'TRUE'
+ if self.parametres['type_tclasse'] == 0 :
+ histo='FALSE'
+ else :
+ histo = 'TRUE'
+ if self.parametres['svg'] :
+ svg = 'TRUE'
+ else :
+ svg = 'FALSE'
+ dendro_path = self.pathout['Rdendro']
+ classe_path = self.pathout['uce']
+ txt = """
+ library(ape)
+ load("%s")
+ source("%s")
+ classes <- read.csv2("%s", row.names=1)
+ classes <- classes[,1]
+ """ % (ffr(dendro_path), ffr(self.parametres['Rgraph']), ffr(classe_path))
+ if self.parametres['dendro'] == 'simple' :
+ txt += """
+ open_file_graph("%s", width=%i, height=%i, svg=%s)
+ plot.dendropr(tree.cut1$tree.cl, classes, type.dendro="%s", histo=%s, bw=%s, lab=NULL, tclasse=%s)
+ """ % (ffr(fileout), width, height, svg, type_dendro, histo, bw, tclasse)
+ elif self.parametres['dendro'] == 'texte' :
+ txt += """
+ load("%s")
+ source("%s")
+ if (is.null(debsup)) {
+ debsup <- debet
+ }
+ chistable <- chistabletot[1:(debsup-1),]
+ """ % (ffr(self.pathout['RData.RData']), ffr(self.parametres['Rgraph']))
+ if self.parametres.get('translation', False) :
+ txt += """
+ rn <- read.csv2("%s", header=FALSE, sep='\t')
+ rnchis <- row.names(chistable)
+ commun <- intersect(rnchis, unique(rn[,2]))
+ idrnchis <- sapply(commun, function(x) {which(rnchis==x)})
+ idrn <- sapply(commun, function(x) {which(as.vector(rn[,2])==x)[1]})
+ rownames(chistable)[idrnchis] <- as.vector(rn[idrn,1])
+ """ % ffr(self.parametres['translation'])
+ txt += """
+ open_file_graph("%s", width=%i, height=%i, svg = %s)
+ plot.dendro.prof(tree.cut1$tree.cl, classes, chistable, nbbycl = 60, type.dendro="%s", bw=%s, lab=NULL)
+ """ % (ffr(fileout), width, height, svg, type_dendro, bw)
+ elif self.parametres['dendro'] == 'cloud' :
+ txt += """
+ load("%s")
+ source("%s")
+ if (is.null(debsup)) {
+ debsup <- debet
+ }
+ chistable <- chistabletot[1:(debsup-1),]
+ open_file_graph("%s", width=%i, height=%i, svg=%s)
+ plot.dendro.cloud(tree.cut1$tree.cl, classes, chistable, nbbycl = 300, type.dendro="%s", bw=%s, lab=NULL)
+ """ % (ffr(self.pathout['RData.RData']), ffr(self.parametres['Rgraph']), ffr(fileout), width, height, svg, type_dendro, bw)
+ self.add(txt)
+ self.write()
+
+
+class ReDoProfScript(PrintRScript) :
+ def make_script(self) :
+ self.sources([self.analyse.parent.RscriptsPath['chdfunct.R']])
+ print self.parametres
+