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()
if self.parametres['film'] :
txt += """
film <- "%s"
- """ % self.pathout['film']
+ """ % ffr(self.pathout['film'])
else :
txt += """
film <- NULL
seuil <- %s
if (!is.null(seuil)) {
if (method!='cooc') {
- seuil <- seuil/100
+ seuil <- seuil/1000
}
}
""" % seuil
"""
class MergeGraphes(PrintRScript) :
- def __init__(self, parametres):
+ def __init__(self, analyse):
self.script = u"#Script genere par IRaMuTeQ - %s\n" % datetime.now().ctime()
self.pathout = PathOut()
- self.parametres = parametres
+ self.parametres = analyse.parametres
self.scriptout = self.pathout['temp']
-
+ self.analyse = analyse
+
def make_script(self) :
#FIXME
-
+
txt = """
library(igraph)
library(Matrix)
V(g)$weight <- (graph.simi$mat.eff/nrow(dm))*100
graphs[['%s']] <- g
"""
- for i, graph in enumerate(self.parametres['lgraphes']) :
+ 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(['/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()
+
+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)
+ """ % (self.pathout['RData.RData'], 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']
+ 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
+ tree.toplot$tip.label <- paste('classe ', tree.toplot$tip.label)
+ plot.phylo(tree.toplot,label.offset=0.1, cex=1.1, no.margin=T)
+ 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']
+ 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()
+
+
projects / iramuteq / blobdiff