log = logging.getLogger('iramuteq.printRscript')
class PrintRScript :
- def __init__ (self, analyse):
+ def __init__ (self, analyse, parametres = None):
log.info('Rscript')
self.pathout = analyse.pathout
self.analyse = analyse
- self.parametres = analyse.parametres
+ if parametres is None :
+ self.parametres = analyse.parametres
+ else :
+ self.parametres = 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()
""" % ffr(DicoPath['TableUc2'])
txt += """
log1 <- "%s"
- #print('FIXME : source newCHD')
- #source('/home/pierre/workspace/iramuteq/Rscripts/newCHD.R')
- #chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path, find='matrix', sample=20, amp=500)
- chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path)#, log.file = log1)
+ print('FIXME : source newCHD')
+ source('/home/pierre/workspace/iramuteq/Rscripts/newCHD.R')
+ chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path, find='matrix', select.next='size', sample=20, amp=500)
+ #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:
if self.param['svg'] : svg = 'TRUE'
else : svg = 'FALSE'
+ if self.param['typegraph'] == 4 :
+ nodesfile = os.path.join(os.path.dirname(self.fileout),'nodes.csv')
+ edgesfile = os.path.join(os.path.dirname(self.fileout),'edges.csv')
+ else :
+ nodesfile = 'NULL'
+ edgesfile = 'NULL'
+
with open(self.RscriptsPath['afc_graph'], 'r') as f:
txt = f.read()
# self.DictPathOut['RData'], \
scripts = txt % (ffr(self.RscriptsPath['Rgraph']),\
self.param['typegraph'], \
+ edgesfile, nodesfile, \
self.param['what'], \
self.param['facteur'][0],\
self.param['facteur'][1], \
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)))
+ layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(12)))
par(mar=c(8,4,1,0))
yp = ifelse(length(toinf), 0.2, 0)
ym = ifelse(length(tominf), 0.2, 0)
"""
txt += """
dm <-readMM(dm.path)
- cn <- read.table(cn.path, sep='\t', quote='"')
+ cn <- read.table(cn.path, sep="\t", quote='"')
colnames(dm) <- cn[,1]
if (file.exists(selected.col)) {
sel.col <- read.csv2(selected.col, header = FALSE)
txt += """
load("%s")
""" % ffr(self.pathout['RData.RData'])
-
+
if self.parametres['coeff'] == 0 :
method = 'cooc'
if not self.parametres['keep_coord'] :
method <- 'cooc'
mat <- make.a(dm)
"""
+ elif self.analyse.indices[self.parametres['coeff']] == 'Jaccard' :
+ method = 'Jaccard'
+ if not self.parametres['keep_coord'] :
+ txt += """
+ method <- 'Jaccard'
+ mat <- sparse.jaccard(dm)
+ """
else :
if not self.parametres['keep_coord'] :
txt += """
method <- 'binomial'
mat <- binom.sim(dm)
"""
- elif self.parametres['coeff'] != 0 :
+ elif self.parametres['coeff'] != 0 and self.analyse.indices[self.parametres['coeff']] != 'Jaccard':
method = self.analyse.indices[self.parametres['coeff']]
if not self.parametres['keep_coord'] :
txt += """
""" % svg
txt += """
vertex.col <- cols
+ col.from.proto <- F
+ if (col.from.proto) {
+ proto.col <- read.table('/tmp/matcol.csv')
+ v.proto.names <- make.names(proto.col[,1])
+ v.proto.col <- as.character(proto.col[,2])
+ v.proto.col[which(v.proto.col=='black')] <- 'yellow'
+ v.names <- V(graph.simi$graph)$name
+ num.color <- sapply(v.names, function(x) {if (x %%in%% v.proto.names) {v.proto.col[which(v.proto.names==x)]} else {'pink'}})
+ vertex.col <- num.color
+ V(graph.simi$graph)$proto.color <- vertex.col
+ }
if (!is.null(graph.simi$com)) {
com <- graph.simi$com
colm <- rainbow(length(com))
}
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')
+ prototypical(mat, mfreq = %s, mrank = %s, cloud = FALSE, cexrange=c(1,2.4), cexalpha= c(0.4, 1), type = '%s', mat.col.path='/tmp/matcol.csv')
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.add(txt)
self.sources([self.analyse.parent.RscriptsPath['simi']])
txt = """
- ng <- merge.graph(graphs)
+ merge.type <- 'proto'
+ if (merge.type == 'normal') {
+ ng <- merge.graph(graphs)
+ } else {
+ ng <- merge.graph.proto(graphs)
+ }
ngraph <- list(graph=ng, layout=layout.fruchterman.reingold(ng, dim=3), labex.cex=V(ng)$weight)
write.graph(ng, "%s", format = 'graphml')
""" % ffr(self.parametres['grapheout'])
rn <- row.names(as.matrix(dist.mat))
open_file_graph("%s", width=1500, height=1000, svg=F)
par(mar=c(10,10,3,3))
- image(1:dim, 1:dim, dst, axes = FALSE, xlab="", ylab="")
+ image(1:dim, 1:dim, dst, axes = FALSE, xlab="", ylab="", col=heat.colors(99), breaks=seq(0.01,1,0.01))
axis(1, 1:dim, rn, cex.axis = 0.9, las=3)
axis(2, 1:dim, rn, cex.axis = 0.9, las=1)
text(expand.grid(1:dim, 1:dim), sprintf("%%0.2f", dst), cex=0.6)
dev.off()
""" % ffr(self.pathout['labbe-matrix.png'])
+ txt += """
+ library(igraph)
+ g <- graph.adjacency(as.matrix(1-dist.mat), mode="lower", weighted=T)
+ write.graph(g, file="%s", format='graphml')
+ open_file_graph("%s", width=1000, height=1000, svg=F)
+ plot(g)
+ dev.off()
+ E(g)$weight <- 1 - E(g)$weight
+ g <- minimum.spanning.tree(g)
+ E(g)$weight <- 1 - E(g)$weight
+ write.graph(g, file="%s", format='graphml')
+ open_file_graph("%s", width=1000, height=1000, svg=F)
+ plot(g)
+ dev.off()
+ """ % (ffr(self.pathout['graph_tot.graphml']), ffr(self.pathout['graph_tot.png']), ffr(self.pathout['graph_min.graphml']), ffr(self.pathout['graph_min.png']))
self.add(txt)
self.write()
self.add(txt)
self.write()
+class DendroScript(PrintRScript) :
+ def make_script(self) :
+ if self.parametres['svg'] :
+ typefile = '.svg'
+ else :
+ typefile = '.png'
+ fileout = self.parametres['fileout']
+ width = self.parametres['width']
+ height = self.parametres['height']
+ type_dendro = self.parametres['dendro_type']
+ if self.parametres['taille_classe'] :
+ tclasse = 'TRUE'
+ else :
+ tclasse = 'FALSE'
+ if self.parametres['color_nb'] == 0 :
+ bw = 'FALSE'
+ else :
+ bw = 'TRUE'
+ if self.parametres['type_tclasse'] == 0 :
+ histo='FALSE'
+ else :
+ histo = 'TRUE'
+ if self.parametres['svg'] :
+ svg = 'TRUE'
+ else :
+ svg = 'FALSE'
+ dendro_path = self.pathout['Rdendro']
+ classe_path = self.pathout['uce']
+ txt = """
+ library(ape)
+ load("%s")
+ source("%s")
+ classes <- read.csv2("%s", row.names=1)
+ classes <- classes[,1]
+ """ % (ffr(dendro_path), ffr(self.parametres['Rgraph']), ffr(classe_path))
+ if self.parametres['dendro'] == 'simple' :
+ txt += """
+ open_file_graph("%s", width=%i, height=%i, svg=%s)
+ plot.dendropr(tree.cut1$tree.cl, classes, type.dendro="%s", histo=%s, bw=%s, lab=NULL, tclasse=%s)
+ """ % (ffr(fileout), width, height, svg, type_dendro, histo, bw, tclasse)
+ elif self.parametres['dendro'] == 'texte' :
+ txt += """
+ load("%s")
+ source("%s")
+ if (is.null(debsup)) {
+ debsup <- debet
+ }
+ chistable <- chistabletot[1:(debsup-1),]
+ """ % (ffr(self.pathout['RData.RData']), ffr(self.parametres['Rgraph']))
+ if self.parametres.get('translation', False) :
+ txt += """
+ rn <- read.csv2("%s", header=FALSE, sep='\t')
+ rnchis <- row.names(chistable)
+ commun <- intersect(rnchis, unique(rn[,2]))
+ idrnchis <- sapply(commun, function(x) {which(rnchis==x)})
+ idrn <- sapply(commun, function(x) {which(as.vector(rn[,2])==x)[1]})
+ rownames(chistable)[idrnchis] <- as.vector(rn[idrn,1])
+ """ % ffr(self.parametres['translation'])
+ txt += """
+ open_file_graph("%s", width=%i, height=%i, svg = %s)
+ plot.dendro.prof(tree.cut1$tree.cl, classes, chistable, nbbycl = 60, type.dendro="%s", bw=%s, lab=NULL)
+ """ % (ffr(fileout), width, height, svg, type_dendro, bw)
+ elif self.parametres['dendro'] == 'cloud' :
+ txt += """
+ load("%s")
+ source("%s")
+ if (is.null(debsup)) {
+ debsup <- debet
+ }
+ chistable <- chistabletot[1:(debsup-1),]
+ open_file_graph("%s", width=%i, height=%i, svg=%s)
+ plot.dendro.cloud(tree.cut1$tree.cl, classes, chistable, nbbycl = 300, type.dendro="%s", bw=%s, lab=NULL)
+ """ % (ffr(self.pathout['RData.RData']), ffr(self.parametres['Rgraph']), ffr(fileout), width, height, svg, type_dendro, bw)
+ self.add(txt)
+ self.write()
+
+
class ReDoProfScript(PrintRScript) :
def make_script(self) :
self.sources([self.analyse.parent.RscriptsPath['chdfunct.R']])
projects / iramuteq / commitdiff