self.pathout = analyse.pathout
self.analyse = analyse
self.parametres = analyse.parametres
+ #self.scriptout = ffr(self.pathout['lastRscript.R'])
self.scriptout = self.pathout['temp']
self.script = u"#Script genere par IRaMuTeQ - %s\n" % datetime.now().ctime()
-
+
def add(self, txt) :
self.script = '\n'.join([self.script, txt])
-
+
def defvar(self, name, value) :
self.add(' <- '.join([name, value]))
data1 <- as(data1, "dgCMatrix")
row.names(data1) <- 1:nrow(data1)
""" % ffr(DicoPath['TableUc1'])
-
+
if classif_mode == 0:
txt += """
data2 <- readMM("%s")
""" % 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)
+ 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)
+ chd2<-CHD(data2, x = nbt, mode.patate = mode.patate, svd.method =
+ svd.method, libsvdc.path = libsvdc.path) log.file = log2)
""" % ffr(DicoPath['log-chd2.txt'])
-
+
txt += """
#lecture des uce
listuce1<-read.csv2("%s")
""" % ffr(DicoPath['listeuce1'])
-
+
if classif_mode == 0:
txt += """
listuce2<-read.csv2("%s")
""" % ffr(DicoPath['listeuce2'])
-
+
txt += """
rm(data1)
"""
-
+
if classif_mode == 0:
txt += """
rm(data2)
write.csv2(n1, file="%s")
rm(n1)
""" % (classif_mode, mincl, ffr(DicoPath['uce']), ffr(DicoPath['n1.csv']))
-
+
txt += """
tree.tot1 <- make_tree_tot(chd1)
# open_file_graph("%s", widt = 600, height=400)
# plot(tree.tot1$tree.cl)
# dev.off()
""" % ffr(DicoPath['arbre1'])
-
+
if classif_mode == 0:
txt += """
classeuce2 <- chd.result$cuce2
# open_file_graph("%s", width = 600, height=400)
# plot(tree.tot2$tree.cl)
# dev.off()
- """ % ffr(DicoPath['arbre2'] )
-
+ """ % ffr(DicoPath['arbre2'] )
+
txt += """
tree.cut1 <- make_dendro_cut_tuple(tree.tot1$dendro_tuple, chd.result$coord_ok, classeuce1, 1, nbt)
save(tree.cut1, file="%s")
-
+
open_file_graph("%s", width = 600, height=400)
plot.dendropr(tree.cut1$tree.cl,classes, histo=TRUE)
open_file_graph("%s", width = 600, height=400)
plot(tree.cut1$dendro_tot_cl)
dev.off()
""" % (ffr(DicoPath['Rdendro']), ffr(DicoPath['dendro1']), ffr(DicoPath['arbre1']))
-
+
if classif_mode == 0:
txt += """
tree.cut2 <- make_dendro_cut_tuple(tree.tot2$dendro_tuple, chd.result$coord_ok, classeuce2, 2, nbt)
plot(tree.cut2$dendro_tot_cl)
dev.off()
""" % (ffr(DicoPath['dendro2']), ffr(DicoPath['arbre2']))
-
+
txt += """
-
+
#save.image(file="%s")
""" % (ffr(DicoPath['RData']))
-
+
fileout = open(DicoPath['Rchdtxt'], 'w')
fileout.write(txt)
fileout.close()
seuil <- %s
if (!is.null(seuil)) {
if (method!='cooc') {
- seuil <- seuil/100
+ seuil <- seuil/1000
}
}
""" % seuil
self.pathout = PathOut()
self.parametres = parametres
self.scriptout = self.pathout['temp']
-
+
def make_script(self) :
#FIXME
-
+
txt = """
library(igraph)
library(Matrix)
RData = os.path.join(path,'RData.RData')
txt += load % (ffr(RData), gname)
self.add(txt)
- self.sources(['/home/pierre/workspace/iramuteq/Rscripts/simi.R'])
+ self.sources([self.analyse.parent.RscriptsPath['simi']])
txt = """
ng <- merge.graph(graphs)
ngraph <- list(graph=ng, layout=layout.fruchterman.reingold(ng, dim=3), labex.cex=V(ng)$weight)
tgen <- read.csv2("%s", row.names = 1, sep = '\\t')
""" % ffr(self.parametres['tgeneff'])
txt += """
+ tgenlem <- read.csv2("%s", row.names = 1, sep = '\\t')
+ """ % ffr(self.parametres['tgenlemeff'])
+ txt += """
res <- build.prof.tgen(tgen)
write.table(res$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):
dev.off()
""" % ffr(self.pathout['barplotrow.png'])
self.add(txt)
- self.write()
\ No newline at end of file
+ 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)
+ """ % (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()
+ """ % (self.pathout['distmat.csv'], self.pathout['dist-labbe.png'])
+ self.add(txt)
+ self.write()
+
+
projects / iramuteq / blobdiff