# -*- coding: utf-8 -*-
#Author: Pierre Ratinaud
#Copyright (c) 2008-2011 Pierre Ratinaud
-#Lisense: GNU/GPL
+#License: GNU/GPL
import tempfile
-from chemins import ffr
+from chemins import ffr, PathOut
import os
import locale
from datetime import datetime
self.pathout = analyse.pathout
self.analyse = analyse
self.parametres = analyse.parametres
+ #self.scriptout = 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]))
def sources(self, lsources) :
for source in lsources :
- self.add('source("%s")' % 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)
- """
+ 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)
- """
- else:
- txt += """
- chd2<-chd1
- """
+ 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")
- """ % 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$dendro_tot_cl)
dev.off()
- """ % (DicoPath['dendro2'], DicoPath['arbre2'])
+ """ % (ffr(DicoPath['dendro2']), ffr(DicoPath['arbre2']))
txt += """
- save.image(file="%s")
- """ % DicoPath['RData']
+
+ #save.image(file="%s")
+ """ % (ffr(DicoPath['RData']))
+
fileout = open(DicoPath['Rchdtxt'], 'w')
fileout.write(txt)
fileout.close()
def RPamTxt(corpus, RscriptPath):
DicoPath = corpus.pathout
param = corpus.parametres
- print param
txt = """
source("%s")
""" % (RscriptPath['pamtxt'])
source("%s")
source("%s")
source("%s")
- """ % (RscriptPath['CHD'], RscriptPath['chdquest'], RscriptPath['anacor'],RscriptPath['Rgraph'])
+ """ % (ffr(RscriptPath['CHD']), ffr(RscriptPath['chdquest']), ffr(RscriptPath['anacor']),ffr(RscriptPath['Rgraph']))
txt += """
nbt <- %i - 1
chd.result<-Rchdquest("%s","%s","%s", nbt = nbt, mincl = mincl)
n1 <- chd.result$n1
classeuce1 <- chd.result$cuce1
- """ % (DicoPath['mat01'], DicoPath['listeuce1'], DicoPath['uce'])
+ """ % (ffr(DicoPath['mat01.csv']), ffr(DicoPath['listeuce1']), ffr(DicoPath['uce']))
txt += """
tree_tot1 <- make_tree_tot(chd.result$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$yminmax[2])
- """ % (DictChdTxtOut['AFC2DSL_OUT'])
+ PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2], active=FALSE)
+ """ % (ffr(DictChdTxtOut['AFC2DSL_OUT']))
txt += """
- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debet, fin=fin, xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2])
- """ % (DictChdTxtOut['AFC2DEL_OUT'])
+ if ((fin - debet) > 2) {
+ PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debet, fin=fin, xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2], active = FALSE)
+ }
+ """ % (ffr(DictChdTxtOut['AFC2DEL_OUT']))
txt += """
- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='coord', xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2])
- """ % (DictChdTxtOut['AFC2DCL_OUT'])
+ PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='coord', xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2], active=FALSE)
+ """ % (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],\
""" % (ffr(dendro),ffr(rgraph), ffr(tmpgraph))
return txt
-def barplot(table, rownames, colnames, rgraph, tmpgraph, intxt = False) :
+def barplot(table, parametres, intxt = False) :
if not intxt :
txttable = 'c(' + ','.join([','.join(line) for line in table]) + ')'
#width = 100 + (15 * len(rownames)) + (100 * len(colnames))
#height = len(rownames) * 15
- rownb = len(rownames)
+ rownb = len(parametres['rownames'])
#if height < 400 :
# height = 400
- rownames = 'c("' + '","'.join(rownames) + '")'
- colnames = 'c("' + '","'.join(colnames) + '")'
+ rownames = 'c("' + '","'.join(parametres['rownames']) + '")'
+ colnames = 'c("' + '","'.join(parametres['colnames']) + '")'
+
if not intxt :
#FIXME
txt = """
""" % (txttable, rownb, rownames, colnames)
else :
txt = intxt
- txt += """
- source("%s")
- color = rainbow(nrow(di))
- width <- 100 + (20*length(rownames(di))) + (100 * length(colnames(di)))
- height <- nrow(di) * 15
- if (height < 400) { height <- 400}
- open_file_graph("%s",width = width, height = height)
- par(mar=c(0,0,0,0))
- layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(7)))
- par(mar=c(2,2,1,0))
- yp = ifelse(length(toinf), 0.2, 0)
- ym = ifelse(length(tominf), 0.2, 0)
- ymin <- ifelse(!length(which(di < 0)), 0, min(di) - ym)
- coord <- barplot(as.matrix(di), beside = TRUE, col = color, space = c(0.1,0.6), ylim=c(ymin, max(di) + yp))
- if (length(toinf)) {
- coordinf <- coord[toinf]
- valinf <- di[toinf]
- text(x=coordinf, y=valinf + 0.1, 'i')
- }
- if (length(tominf)) {
- coordinf <- coord[toinf]
- valinf <- di[toinf]
- text(x=coordinf, y=valinf - 0.1, 'i')
- }
- c <- colMeans(coord)
- c1 <- c[-1]
- c2 <- c[-length(c)]
- cc <- cbind(c1,c2)
- lcoord <- apply(cc, 1, mean)
- abline(v=lcoord)
- if (min(di) < 0) {
- amp <- abs(max(di) - min(di))
- } else {
- amp <- max(di)
- }
- if (amp < 10) {
- d <- 2
- } else {
- d <- signif(amp%%/%%10,1)
- }
- mn <- round(min(di))
- mx <- round(max(di))
- for (i in mn:mx) {
- if ((i/d) == (i%%/%%d)) {
- abline(h=i,lty=3)
+ if not 'tree' in parametres :
+ txt += """
+ source("%s")
+ color = rainbow(nrow(di))
+ width <- %i
+ height <- %i
+ open_file_graph("%s",width = width, height = height, svg = %s)
+ par(mar=c(0,0,0,0))
+ layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(7)))
+ par(mar=c(8,4,1,0))
+ yp = ifelse(length(toinf), 0.2, 0)
+ ym = ifelse(length(tominf), 0.2, 0)
+ ymin <- ifelse(!length(which(di < 0)), 0, min(di) - ym)
+ coord <- barplot(as.matrix(di), beside = TRUE, col = color, space = c(0.1,0.6), ylim=c(ymin, max(di) + yp), las = 2)
+ if (length(toinf)) {
+ coordinf <- coord[toinf]
+ valinf <- di[toinf]
+ text(x=coordinf, y=valinf + 0.1, 'i')
}
- }
- par(mar=c(0,0,0,0))
- plot(0, axes = FALSE, pch = '')
- legend(x = 'center' , rownames(di), fill = color)
- dev.off()
- """ % (rgraph, ffr(tmpgraph))
+ if (length(tominf)) {
+ coordinf <- coord[toinf]
+ valinf <- di[toinf]
+ text(x=coordinf, y=valinf - 0.1, 'i')
+ }
+ c <- colMeans(coord)
+ c1 <- c[-1]
+ c2 <- c[-length(c)]
+ cc <- cbind(c1,c2)
+ lcoord <- apply(cc, 1, mean)
+ abline(v=lcoord)
+ if (min(di) < 0) {
+ amp <- abs(max(di) - min(di))
+ } else {
+ amp <- max(di)
+ }
+ if (amp < 10) {
+ d <- 2
+ } else {
+ d <- signif(amp%%/%%10,1)
+ }
+ mn <- round(min(di))
+ mx <- round(max(di))
+ for (i in mn:mx) {
+ if ((i/d) == (i%%/%%d)) {
+ abline(h=i,lty=3)
+ }
+ }
+ par(mar=c(0,0,0,0))
+ plot(0, axes = FALSE, pch = '')
+ legend(x = 'center' , rownames(di), fill = color)
+ dev.off()
+ """ % (ffr(parametres['rgraph']), parametres['width'], parametres['height'], ffr(parametres['tmpgraph']), parametres['svg'])
+ else :
+ txt += """
+ load("%s")
+ library(ape)
+ source("%s")
+ width = %i
+ height = %i
+ open_file_graph("%s", width=width, height=height, svg = %s)
+ plot.dendro.lex(tree.cut1$tree.cl, di)
+ """ % (ffr(parametres['tree']), ffr(parametres['rgraph']), parametres['width'], parametres['height'], ffr(parametres['tmpgraph']), parametres['svg'])
return txt
#def RAfcUci(DictAfcUciOut, nd=2, RscriptsPath='', PARCEX='0.8'):
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
dm <-readMM(dm.path)
cn <- read.table(cn.path, sep='\t', quote='"')
colnames(dm) <- cn[,1]
- sel.col <- read.csv2(selected.col, header = FALSE)
- sel.col <- sel.col[,1] + 1
+ if (file.exists(selected.col)) {
+ sel.col <- read.csv2(selected.col, header = FALSE)
+ sel.col <- sel.col[,1] + 1
+ } else {
+ sel.col <- 1:ncol(dm)
+ }
if (!word) {
dm <- dm[, sel.col]
} else {
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
txt += """
dm <-read.csv2(dm.path)
dm <- as.matrix(dm)
- sel.col <- read.csv2(selected.col, header = FALSE)
- sel.col <- sel.col[,1] + 1
+ if (file.exists(selected.col)) {
+ sel.col <- read.csv2(selected.col, header = FALSE)
+ sel.col <- sel.col[,1] + 1
+ } else {
+ sel.col <- 1:ncol(dm)
+ }
if (!word) {
dm <- dm[, sel.col]
} else {
else :
txt += """
load("%s")
- """ % self.pathout['RData.RData']
+ """ % ffr(self.pathout['RData.RData'])
if self.parametres['coeff'] == 0 :
method = 'cooc'
if self.parametres['type_graph'] == 1 :
graphnb = 1
type = 'nplot'
- dirout = os.path.dirname(self.pathout['mat01'])
+ dirout = os.path.dirname(self.pathout['mat01.csv'])
while os.path.exists(os.path.join(dirout,'graph_simi_'+str(graphnb)+'.png')):
graphnb +=1
self.filename = ffr(os.path.join(dirout,'graph_simi_'+str(graphnb)+'.png'))
if self.parametres['type_graph'] == 2 : type = 'rgl'
+ if self.parametres['type_graph'] == 3 :
+ graphnb = 1
+ type = 'web'
+ dirout = os.path.dirname(self.pathout['mat01.csv'])
+ 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)
+ self.filename = os.path.join(self.filename, 'gexf.gexf')
+ if self.parametres['type_graph'] == 4 :
+ graphnb = 1
+ type = 'rglweb'
+ dirout = os.path.dirname(self.pathout['mat01.csv'])
+ while os.path.exists(os.path.join(dirout,'webrgl_'+str(graphnb))):
+ graphnb +=1
+ self.filename = ffr(os.path.join(dirout,'webrgl_'+str(graphnb)))
+ os.mkdir(self.filename)
if self.parametres['arbremax'] :
arbremax = 'TRUE'
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/1000
+ }
+ }
""" % 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 :
txt+="""
- label.cex <- NULL
+ label.cex <- cex
"""
if self.parametres.get('sfromchi', False) :
txt += """
vertex.size <- NULL
"""
else :
- if self.parametres['type'] == 'clustersimitxt' :
+ #print 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])
"""
else :
txt += """
if (is.null(vcexminmax[1])) {
- label.cex <- NULL
+ label.cex <- cex
} else {
label.cex <- graph.simi$label.cex
}
"""
- if self.parametres['type'] == 'clustersimitxt' 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()
self.packages(['wordcloud'])
bg_col = Rcolor(self.parametres['col_bg'])
txt_col = Rcolor(self.parametres['col_text'])
+ if self.parametres['svg'] :
+ svg = 'TRUE'
+ else :
+ svg = 'FALSE'
txt = """
+ svg <- %s
+ """ % svg
+ txt += """
act <- read.csv2("%s", header = FALSE, row.names=1, sep='\t')
selected.col <- read.table("%s")
toprint <- as.matrix(act[selected.col[,1] + 1,])
toprint <- as.matrix(toprint[order(toprint[,1], decreasing=TRUE),])
toprint <- as.matrix(toprint[1:maxword,])
}
- open_file_graph("%s", width = %i, height = %i)
+ open_file_graph("%s", width = %i, height = %i , svg = svg)
par(bg=rgb%s)
wordcloud(row.names(toprint), toprint[,1], scale=c(%f,%f), random.order=FALSE, colors=rgb%s)
dev.off()
""" % (ffr(self.analyse.pathout['actives_eff.csv']), ffr(self.analyse.pathout['selected.csv']), self.parametres['maxword'], ffr(self.parametres['graphout']), self.parametres['width'], self.parametres['height'], bg_col, self.parametres['maxcex'], self.parametres['mincex'], txt_col)
self.add(txt)
self.write()
+
+class ProtoScript(PrintRScript) :
+ 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))
+ }
+ errort <- function(x) {
+ qt(0.975,df=lenght(x)-1)*sd(x)/sqrt(lenght(x))
+ }
+ 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), type = '%s')
+ dev.off()
+ """ % (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()
+
+
+class ExportAfc(PrintRScript) :
+ def make_script(self) :
+ self.source([self.analyse.parent.RscriptsPath['Rgraph']])
+ self.packages(['rgexf'])
+ 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)$weight)
+ write.graph(ng, "%s", format = 'graphml')
+ """ % ffr(self.parametres['grapheout'])
+ self.add(txt)
+
+class TgenSpecScript(PrintRScript):
+ def make_script(self):
+ self.packages(['textometry'])
+ txt = """
+ tgen <- read.csv2("%s", row.names = 1, sep = '\\t')
+ """ % ffr(self.parametres['tgeneff'])
+ txt += """
+ tot <- tgen[nrow(tgen), ]
+ result <- NULL
+ tgen <- tgen[-nrow(tgen),]
+ for (i in 1:nrow(tgen)) {
+ mat <- rbind(tgen[i,], tot - tgen[i,])
+ specmat <- specificities(mat)
+ result <- rbind(result, specmat[1,])
+ }
+ colnames(result) <- colnames(tgen)
+ row.names(result) <- rownames(tgen)
+ write.table(result, file = "%s", sep='\\t', col.names = NA)
+ """ % ffr(self.pathout['tgenspec.csv'])
+ self.add(txt)
+
+class TgenProfScript(PrintRScript):
+ def make_script(self):
+ self.sources([self.analyse.ira.RscriptsPath['chdfunct']])
+ txt = """
+ tgen <- read.csv2("%s", row.names = 1, sep = '\\t')
+ """ % ffr(self.parametres['tgeneff'])
+ txt += """
+ tgenlem <- read.csv2("%s", row.names = 1, sep = '\\t')
+ """ % ffr(self.parametres['tgenlemeff'])
+ txt += """
+ res <- build.prof.tgen(tgen)
+ write.table(res$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):
+ 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()
projects / iramuteq / blobdiff