def sources(self, lsources) :
for source in lsources :
- self.add('source("%s", encoding = \'utf8\')' % source)
+ self.add('source("%s", encoding = \'utf8\')' % ffr(source))
def packages(self, lpks) :
for pk in lpks :
def load(self, l) :
for val in l :
- self.add('load("%s")' % val)
+ self.add('load("%s")' % ffr(val))
def write(self) :
with open(self.scriptout, 'w') as f :
source("%s")
source("%s")
source("%s")
- """ % (RscriptPath['CHD'], RscriptPath['chdtxt'], RscriptPath['anacor'], RscriptPath['Rgraph'])
+ """ % (ffr(RscriptPath['CHD']), ffr(RscriptPath['chdtxt']), ffr(RscriptPath['anacor']), ffr(RscriptPath['Rgraph']))
if R_max_mem :
txt += """
memory.limit(%i)
data1 <- readMM("%s")
data1 <- as(data1, "dgCMatrix")
row.names(data1) <- 1:nrow(data1)
- """ % DicoPath['TableUc1']
+ """ % ffr(DicoPath['TableUc1'])
if classif_mode == 0:
txt += """
data2 <- readMM("%s")
data2 <- as(data2, "dgCMatrix")
row.names(data2) <- 1:nrow(data2)
- """ % DicoPath['TableUc2']
+ """ % ffr(DicoPath['TableUc2'])
txt += """
chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path)
"""
txt += """
chd2<-CHD(data2, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path)
"""
- else:
- txt += """
- chd2<-chd1
- """
txt += """
#lecture des uce
listuce1<-read.csv2("%s")
- """ % DicoPath['listeuce1']
+ """ % ffr(DicoPath['listeuce1'])
if classif_mode == 0:
txt += """
listuce2<-read.csv2("%s")
- """ % DicoPath['listeuce2']
+ """ % ffr(DicoPath['listeuce2'])
txt += """
rm(data1)
}
n1 <- chd.result$n1
classeuce1 <- chd.result$cuce1
- classeuce2 <- chd.result$cuce2
- """ % (classif_mode, mincl, DicoPath['uce'])
+ classes<-n1[,ncol(n1)]
+ write.csv2(n1, file="%s")
+ rm(n1)
+ """ % (classif_mode, mincl, ffr(DicoPath['uce']), ffr(DicoPath['n1.csv']))
txt += """
tree.tot1 <- make_tree_tot(chd1)
# open_file_graph("%s", widt = 600, height=400)
# plot(tree.tot1$tree.cl)
# dev.off()
- """%DicoPath['arbre1']
+ """ % ffr(DicoPath['arbre1'])
if classif_mode == 0:
txt += """
+ classeuce2 <- chd.result$cuce2
tree.tot2 <- make_tree_tot(chd2)
# open_file_graph("%s", width = 600, height=400)
# plot(tree.tot2$tree.cl)
# dev.off()
- """ % 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")
- classes<-n1[,ncol(n1)]
+
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()
- """ % (DicoPath['Rdendro'], DicoPath['dendro1'], DicoPath['arbre1'])
+ """ % (ffr(DicoPath['Rdendro']), ffr(DicoPath['dendro1']), ffr(DicoPath['arbre1']))
if classif_mode == 0:
txt += """
plot(tree.cut2$tree.cl)
dev.off()
open_file_graph("%s", width = 600, height=400)
- plot(tree.cut1$dendro_tot_cl)
+ plot(tree.cut2$dendro_tot_cl)
dev.off()
- """ % (DicoPath['dendro2'], DicoPath['arbre2'])
+ """ % (ffr(DicoPath['dendro2']), ffr(DicoPath['arbre2']))
txt += """
- save.image(file="%s")
- """ % DicoPath['RData']
+
+ #save.image(file="%s")
+ """ % (ffr(DicoPath['RData']))
+
fileout = open(DicoPath['Rchdtxt'], 'w')
fileout.write(txt)
fileout.close()
source("%s")
source("%s")
source("%s")
- """ % (RscriptPath['CHD'], RscriptPath['chdquest'], RscriptPath['anacor'],RscriptPath['Rgraph'])
+ """ % (ffr(RscriptPath['CHD']), ffr(RscriptPath['chdquest']), ffr(RscriptPath['anacor']),ffr(RscriptPath['Rgraph']))
txt += """
nbt <- %i - 1
chd.result<-Rchdquest("%s","%s","%s", nbt = nbt, mincl = mincl)
n1 <- chd.result$n1
classeuce1 <- chd.result$cuce1
- """ % (DicoPath['mat01.csv'], DicoPath['listeuce1'], DicoPath['uce'])
+ """ % (ffr(DicoPath['mat01.csv']), ffr(DicoPath['listeuce1']), ffr(DicoPath['uce']))
txt += """
tree_tot1 <- make_tree_tot(chd.result$chd)
open_file_graph("%s", width = 600, height=400)
plot(tree_tot1$tree.cl)
dev.off()
- """%DicoPath['arbre1']
+ """ % ffr(DicoPath['arbre1'])
txt += """
tree_cut1 <- make_dendro_cut_tuple(tree_tot1$dendro_tuple, chd.result$coord_ok, classeuce1, 1, nbt)
open_file_graph("%s", width = 600, height=400)
classes<-n1[,ncol(n1)]
plot.dendropr(tree_cut1$tree.cl,classes, histo = TRUE)
- """ % (DicoPath['Rdendro'],DicoPath['dendro1'])
+ """ % (ffr(DicoPath['Rdendro']), ffr(DicoPath['dendro1']))
txt += """
save.image(file="%s")
- """ % DicoPath['RData']
+ """ % ffr(DicoPath['RData'])
fileout = open(DicoPath['Rchdquest'], 'w')
fileout.write(txt)
fileout.close()
-def AlcesteTxtProf(DictChdTxtOut, RscriptsPath, clnb, taillecar):
+def ReinertTxtProf(DictChdTxtOut, RscriptsPath, clnb, taillecar):
txt = "clnb<-%i\n" % clnb
txt += """
source("%s")
-load("%s")
-""" % (RscriptsPath['chdfunct'], DictChdTxtOut['RData'])
+#load("%s")
+n1 <- read.csv2("%s")
+""" % (ffr(RscriptsPath['chdfunct']), ffr(DictChdTxtOut['RData']), ffr(DictChdTxtOut['n1.csv']))
txt += """
dataact<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
datasup<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
dataet<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
-""" % (DictChdTxtOut['Contout'], DictChdTxtOut['ContSupOut'], DictChdTxtOut['ContEtOut'])
+""" % (ffr(DictChdTxtOut['Contout']), ffr(DictChdTxtOut['ContSupOut']), ffr(DictChdTxtOut['ContEtOut']))
txt += """
tablesqrpact<-BuildProf(as.matrix(dataact),n1,clnb)
tablesqrpsup<-BuildProf(as.matrix(datasup),n1,clnb)
"""
txt += """
PrintProfile(n1,tablesqrpact[4],tablesqrpet[4],tablesqrpact[5],tablesqrpet[5],clnb,"%s","%s",tablesqrpsup[4],tablesqrpsup[5])
-""" % (DictChdTxtOut['PROFILE_OUT'], DictChdTxtOut['ANTIPRO_OUT'])
+""" % (ffr(DictChdTxtOut['PROFILE_OUT']), ffr(DictChdTxtOut['ANTIPRO_OUT']))
txt += """
colnames(tablesqrpact[[2]])<-paste('classe',1:clnb,sep=' ')
colnames(tablesqrpact[[1]])<-paste('classe',1:clnb,sep=' ')
write.csv2(ptabletot,file="%s")
gbcluster<-n1
write.csv2(gbcluster,file="%s")
-""" % (DictChdTxtOut['chisqtable'], DictChdTxtOut['ptable'], DictChdTxtOut['SbyClasseOut'])
+""" % (ffr(DictChdTxtOut['chisqtable']), ffr(DictChdTxtOut['ptable']), ffr(DictChdTxtOut['SbyClasseOut']))
if clnb > 2 :
txt += """
library(ca)
#FIXME : split this!!!
txt += """
source("%s")
- """ % RscriptsPath['Rgraph']
+ """ % ffr(RscriptsPath['Rgraph'])
txt += """
afc <- summary.ca.dm(afc)
write.csv2(afc_table$facteur, file = "%s")
write.csv2(afc_table$colonne, file = "%s")
write.csv2(afc_table$ligne, file = "%s")
- """ % (DictChdTxtOut['afc_facteur'], DictChdTxtOut['afc_col'], DictChdTxtOut['afc_row'])
+ """ % (ffr(DictChdTxtOut['afc_facteur']), ffr(DictChdTxtOut['afc_col']), ffr(DictChdTxtOut['afc_row']))
txt += """
PARCEX<-%s
""" % taillecar
txt += """
xyminmax <- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
- """ % (DictChdTxtOut['AFC2DL_OUT'])
+ """ % (ffr(DictChdTxtOut['AFC2DL_OUT']))
txt += """
PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2], active=FALSE)
- """ % (DictChdTxtOut['AFC2DSL_OUT'])
+ """ % (ffr(DictChdTxtOut['AFC2DSL_OUT']))
txt += """
if ((fin - debet) > 2) {
PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debet, fin=fin, xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2], active = FALSE)
}
- """ % (DictChdTxtOut['AFC2DEL_OUT'])
+ """ % (ffr(DictChdTxtOut['AFC2DEL_OUT']))
txt += """
PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='coord', xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2], active=FALSE)
- """ % (DictChdTxtOut['AFC2DCL_OUT'])
+ """ % (ffr(DictChdTxtOut['AFC2DCL_OUT']))
# txt += """
# PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
# PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab)
rm(tablesqrpsup)
rm(tablesqrpet)
save.image(file="%s")
-""" % DictChdTxtOut['RData']
+""" % ffr(DictChdTxtOut['RData'])
file = open(DictChdTxtOut['RTxtProfGraph'], 'w')
file.write(txt)
file.close()
txt = f.read()
# self.DictPathOut['RData'], \
- scripts = txt % (self.RscriptsPath['Rgraph'],\
+ scripts = txt % (ffr(self.RscriptsPath['Rgraph']),\
self.param['typegraph'], \
self.param['what'], \
self.param['facteur'][0],\
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':
+ 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"
- """ % (self.pathout['mat01.csv'], self.pathout['actives.csv'], self.pathout['selected.csv'])
+ """ % (ffr(self.pathout['mat01.csv']), ffr(self.pathout['actives.csv']), ffr(self.pathout['selected.csv']))
if 'word' in self.parametres :
txt += """
word <- TRUE
index <- which(colnames(dm) == forme)
}
"""
- elif not self.parametres['keep_coord'] and self.parametres['type'] == 'simimatrix' :
+ elif not self.parametres['keep_coord'] and (self.parametres['type'] == 'simimatrix' or self.parametres['type'] == 'simiclustermatrix'):
txt += """
dm.path <- "%s"
selected.col <- "%s"
- """ % (self.pathout['mat01.csv'], self.pathout['selected.csv'])
+ """ % (ffr(self.pathout['mat01.csv']), ffr(self.pathout['selected.csv']))
if 'word' in self.parametres :
txt += """
word <- TRUE
else :
txt += """
load("%s")
- """ % self.pathout['RData.RData']
+ """ % ffr(self.pathout['RData.RData'])
if self.parametres['coeff'] == 0 :
method = 'cooc'
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 += """
seuil <- %s
+ if (!is.null(seuil)) {
+ if (method!='cooc') {
+ seuil <- seuil/100
+ }
+ }
""" % seuil
txt += """
cols <- vertex.label.color
chivertex.size <- norm.vec(toblack, vcexminmax[1], vcexminmax[2])
- """ % (self.analyse.parent.RscriptsPath['chdfunct'])
+ """ % (ffr(self.analyse.parent.RscriptsPath['chdfunct']))
else :
txt += """
vertex.label.color <- 'black'
"""
else :
#print self.parametres
- if (self.parametres['type'] == 'clustersimitxt' and self.parametres.get('tmpchi', False)) or (self.parametres['type'] == 'simimatrix' and 'tmpchi' in 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]
txt += """
lchi <- lchi[sel.col]
"""
- if self.parametres['type'] == 'clustersimitxt' and self.parametres.get('cexfromchi', False) :
+ if self.parametres['type'] in ['clustersimitxt', 'simimatrix', 'simiclustermatrix'] and self.parametres.get('cexfromchi', False) :
txt += """
label.cex <- norm.vec(lchi, vcexminmax[1], vcexminmax[2])
"""
label.cex <- graph.simi$label.cex
}
"""
- if (self.parametres['type'] == 'clustersimitxt' or self.parametres['type'] == 'simimatrix') and self.parametres.get('sfromchi', False):
+ 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
vertex.label.color <- colm[membership(com)]
}
}
- 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, svg = svg)
+ 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, self.pathout['RData'])
+ """ % (type, self.filename, ffr(self.pathout['RData']))
self.add(txt)
self.write()
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))
}
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))
+ 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.analyse.pathout['table.csv'], self.analyse.pathout['proto.png'], self.parametres['limfreq'], self.parametres['limrang'], self.parametres['typegraph'])
self.add(txt)
self.write()
self.packages(['textometry'])
txt = """
tgen <- read.csv2("%s", row.names = 1, sep = '\\t')
- """ % self.parametres['tgeneff']
+ """ % ffr(self.parametres['tgeneff'])
txt += """
tot <- tgen[nrow(tgen), ]
result <- NULL
colnames(result) <- colnames(tgen)
row.names(result) <- rownames(tgen)
write.table(result, file = "%s", sep='\\t', col.names = NA)
- """ % self.pathout['tgenspec.csv']
+ """ % 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 += """
+ 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']))
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()
\ No newline at end of file
projects / iramuteq / blobdiff