""" % ffr(DicoPath['TableUc2'])
txt += """
log1 <- "%s"
- chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method =
- svd.method, libsvdc.path = libsvdc.path, log.file = log1)
+ #print('FIXME : source newCHD')
+ #source('/home/pierre/workspace/iramuteq/Rscripts/newCHD.R')
+ #chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path, find='matrix', sample=20, amp=500)
+ chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path)#, log.file = log1)
""" % ffr(DicoPath['log-chd1.txt'])
if classif_mode == 0:
txt += """
log2 <- "%s"
chd2<-CHD(data2, x = nbt, mode.patate = mode.patate, svd.method =
- svd.method, libsvdc.path = libsvdc.path) log.file = log2)
+ svd.method, libsvdc.path = libsvdc.path)#, log.file = log2)
""" % ffr(DicoPath['log-chd2.txt'])
txt += """
txt += """
classif_mode <- %i
mincl <- %i
+ if (mincl == 0) {mincl <- round(nrow(chd1$n1)/(nbt+1))}
uceout <- "%s"
+ write.csv2(chd1$n1, file="%s")
if (classif_mode == 0) {
chd.result <- Rchdtxt(uceout, chd1, chd2 = chd2, mincl = mincl,classif_mode = classif_mode, nbt = nbt)
+ classeuce1 <- chd.result$cuce1
+ tree.tot1 <- make_tree_tot(chd1)
+ tree.cut1 <- make_dendro_cut_tuple(tree.tot1$dendro_tuple, chd.result$coord_ok, classeuce1, 1, nbt)
+
} else {
- chd.result <- Rchdtxt(uceout, chd1, chd2 = chd1, mincl = mincl,classif_mode = classif_mode, nbt = nbt)
+ #chd.result <- Rchdtxt(uceout, chd1, chd2 = chd1, mincl = mincl,classif_mode = classif_mode, nbt = nbt)
+ tree.tot1 <- make_tree_tot(chd1)
+ terminales <- find.terminales(chd1$n1, chd1$list_mere, chd1$list_fille, mincl)
+ tree.cut1 <- make.classes(terminales, chd1$n1, tree.tot1$tree.cl, chd1$list_fille)
+ write.csv2(tree.cut1$n1, uceout)
+ chd.result <- tree.cut1
}
- n1 <- chd.result$n1
- classeuce1 <- chd.result$cuce1
- classes<-n1[,ncol(n1)]
- write.csv2(n1, file="%s")
- rm(n1)
- """ % (classif_mode, mincl, ffr(DicoPath['uce']), ffr(DicoPath['n1.csv']))
+ classes<-chd.result$n1[,ncol(chd.result$n1)]
+ write.csv2(chd.result$n1, file="%s")
+ """ % (classif_mode, mincl, ffr(DicoPath['uce']), ffr(DicoPath['n1-1.csv']), ffr(DicoPath['n1.csv']))
txt += """
- tree.tot1 <- make_tree_tot(chd1)
+# tree.tot1 <- make_tree_tot(chd1)
# open_file_graph("%s", widt = 600, height=400)
# plot(tree.tot1$tree.cl)
# dev.off()
""" % ffr(DicoPath['arbre2'] )
txt += """
- tree.cut1 <- make_dendro_cut_tuple(tree.tot1$dendro_tuple, chd.result$coord_ok, classeuce1, 1, nbt)
- save(tree.cut1, file="%s")
+ save(tree.cut1, file="%s")
open_file_graph("%s", width = 600, height=400)
plot.dendropr(tree.cut1$tree.cl,classes, histo=TRUE)
dataet<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
""" % (ffr(DictChdTxtOut['Contout']), ffr(DictChdTxtOut['ContSupOut']), ffr(DictChdTxtOut['ContEtOut']))
txt += """
-tablesqrpact<-BuildProf(as.matrix(dataact),n1,clnb)
-tablesqrpsup<-BuildProf(as.matrix(datasup),n1,clnb)
-tablesqrpet<-BuildProf(as.matrix(dataet),n1,clnb)
+print('ATTENTION NEW BUILD PROF')
+#tablesqrpact<-BuildProf(as.matrix(dataact),n1,clnb)
+#tablesqrpsup<-BuildProf(as.matrix(datasup),n1,clnb)
+#tablesqrpet<-BuildProf(as.matrix(dataet),n1,clnb)
+tablesqrpact<-new.build.prof(as.matrix(dataact),n1,clnb)
+tablesqrpsup<-new.build.prof(as.matrix(datasup),n1,clnb)
+tablesqrpet<-new.build.prof(as.matrix(dataet),n1,clnb)
+
"""
txt += """
PrintProfile(n1,tablesqrpact[4],tablesqrpet[4],tablesqrpact[5],tablesqrpet[5],clnb,"%s","%s",tablesqrpsup[4],tablesqrpsup[5])
else :
txt += """
word <- FALSE
+ index <- NULL
"""
txt += """
dm <-readMM(dm.path)
txt += """
mat <- graph.word(mat, index)
cs <- colSums(mat)
- if (length(cs)) mat <- mat[,-which(cs==0)]
+ if (length(which(cs==0))) mat <- mat[,-which(cs==0)]
rs <- rowSums(mat)
- if (length(rs)) mat <- mat[-which(rs==0),]
- if (length(cs)) dm <- dm[, -which(cs==0)]
+ 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'] == 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=''
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)
+ os.mkdir(self.filename)
self.filename = os.path.join(self.filename, 'gexf.gexf')
if self.parametres['type_graph'] == 4 :
graphnb = 1
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)
+ 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) :
self.analyse.parent.RscriptsPath['Rgraph']])
txt = """
tab <- read.csv2("%s", header=TRUE, sep=';', row.names=1)
- """ % (self.pathout['tableafcm.csv'])
+ """ % (ffr(self.pathout['tableafcm.csv']))
txt += """
dist.mat <- dist.labbe(tab)
dist.mat <- as.dist(dist.mat, upper=F, diag=F)
par(cex=1.2)
plot.phylo(as.phylo(chd), type='unrooted', lab4ut="axial")
dev.off()
- """ % (self.pathout['distmat.csv'], self.pathout['dist-labbe.png'])
+ """ % (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="")
+ 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'])
self.add(txt)
self.write()
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
- tree.toplot$tip.label <- paste('classe ', tree.toplot$tip.label)
- plot.phylo(tree.toplot,label.offset=0.1, cex=1.1, no.margin=T)
+ 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))
ptc <- tcp/sum(tcp)
dpt <- t(dpt)
dd <- dpt
- """ % self.parametres['var']
+ """ % self.parametres['var'].replace(u'*', u"\\\\*")
txt += """
classes <- n1[,ncol(n1)]
tcl <- table(classes)
self.add(txt)
self.write()
+class ReDoProfScript(PrintRScript) :
+ def make_script(self) :
+ self.sources([self.analyse.parent.RscriptsPath['chdfunct.R']])
+ print self.parametres
projects / iramuteq / blobdiff