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")
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"
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"
"""
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$label.cex
}
"""
- if (self.parametres['type'] == 'clustersimitxt' or self.parametres['type'] == 'simimatrix') and self.parametres.get('sfromchi', False):
+ if (self.parametres['type'] in ['clustersimitxt', 'simimatrix', 'simiclustermatrix']) and self.parametres.get('sfromchi', False):
txt += """
vertex.size <- norm.vec(lchi, minmaxeff[1], minmaxeff[2])
if (!length(vertex.size)) vertex.size <- 0
""" % ffr(self.pathout['tgenspec.csv'])
self.add(txt)
+class TgenProfScript(PrintRScript):
+ def make_script(self):
+ self.sources([self.analyse.ira.RscriptsPath['chdfunct']])
+ txt = """
+ tgen <- read.csv2("%s", row.names = 1, sep = '\\t')
+ """ % ffr(self.parametres['tgeneff'])
+ txt += """
+ res <- build.prof.tgen(tgen)
+ write.table(res$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']])