X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=PrintRScript.py;h=be81a14f83f627d69df85a589b1aaec710f1ea3c;hp=deaddf51ced131c513700e1eda655a5e86b25a58;hb=4c4a0f5c8a9c145bc81fa93df5d1b0af34399eaf;hpb=3337f787ca0fe81614a3957d8fe332a7d44a14bc diff --git a/PrintRScript.py b/PrintRScript.py index deaddf5..be81a14 100644 --- a/PrintRScript.py +++ b/PrintRScript.py @@ -4,7 +4,7 @@ #License: GNU/GPL import tempfile -from chemins import ffr +from chemins import ffr, PathOut import os import locale from datetime import datetime @@ -18,12 +18,13 @@ class PrintRScript : 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])) @@ -154,7 +155,7 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv data1 <- as(data1, "dgCMatrix") row.names(data1) <- 1:nrow(data1) """ % ffr(DicoPath['TableUc1']) - + if classif_mode == 0: txt += """ data2 <- readMM("%s") @@ -162,28 +163,32 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv row.names(data2) <- 1:nrow(data2) """ % ffr(DicoPath['TableUc2']) txt += """ - chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path) - """ - + log1 <- "%s" + 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 += """ - chd2<-CHD(data2, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path) - """ - + log2 <- "%s" + 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) @@ -203,14 +208,14 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv 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 @@ -218,19 +223,19 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv # 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$coord_ok, classeuce2, 2, nbt) @@ -241,12 +246,12 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv plot(tree.cut2$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() @@ -944,7 +949,7 @@ class PrintSimiScript(PrintRScript) : seuil <- %s if (!is.null(seuil)) { if (method!='cooc') { - seuil <- seuil/100 + seuil <- seuil/1000 } } """ % seuil @@ -1189,7 +1194,7 @@ class ProtoScript(PrintRScript) : 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') dev.off() - """ % (self.analyse.pathout['table.csv'], self.analyse.pathout['proto.png'], self.parametres['limfreq'], self.parametres['limrang'], self.parametres['typegraph']) + """ % (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() @@ -1201,6 +1206,41 @@ class ExportAfc(PrintRScript) : txt = """ """ +class MergeGraphes(PrintRScript) : + def __init__(self, parametres): + self.script = u"#Script genere par IRaMuTeQ - %s\n" % datetime.now().ctime() + self.pathout = PathOut() + self.parametres = parametres + self.scriptout = self.pathout['temp'] + + def make_script(self) : + #FIXME + + txt = """ + library(igraph) + library(Matrix) + graphs <- list() + """ + load = """ + load("%s") + g <- graph.simi$graph + V(g)$weight <- (graph.simi$mat.eff/nrow(dm))*100 + graphs[['%s']] <- g + """ + for i, graph in enumerate(self.parametres['lgraphes']) : + path = os.path.dirname(graph) + gname = ''.join(['g', `i`]) + RData = os.path.join(path,'RData.RData') + txt += load % (ffr(RData), gname) + self.add(txt) + self.sources([self.analyse.parent.RscriptsPath['simi']]) + txt = """ + ng <- merge.graph(graphs) + ngraph <- list(graph=ng, layout=layout.fruchterman.reingold(ng, dim=3), labex.cex=V(ng)$weight) + write.graph(ng, "%s", format = 'graphml') + """ % ffr(self.parametres['grapheout']) + self.add(txt) + class TgenSpecScript(PrintRScript): def make_script(self): self.packages(['textometry']) @@ -1229,10 +1269,18 @@ class TgenProfScript(PrintRScript): 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): @@ -1259,4 +1307,28 @@ 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() + +