Nothing
`clustermap` <- function(sp.obj, names.var, clustnum, method=c("kmeans","hclust"),type=NULL, centers=NULL, scale=FALSE,
names.arg="", names.attr=names(sp.obj), criteria=NULL, carte=NULL, identify=FALSE, cex.lab=0.8, pch=16,
col="lightblue3", xlab="Cluster", ylab="Number", axes=FALSE, lablong="", lablat="")
{
envir = as.environment(1)
# Verification of the Spatial Object sp.obj
class.obj<-class(sp.obj)[1]
if(substr(class.obj,1,7)!="Spatial") stop("sp.obj may be a Spatial object")
if(substr(class.obj,nchar(class.obj)-8,nchar(class.obj))!="DataFrame") stop("sp.obj should contain a data.frame")
if(!is.numeric(names.var) & length(match(names.var,names(sp.obj)))!=length(names.var) ) stop("At least one component of names.var is not included in the data.frame of sp.obj")
if(length(names.attr)!=length(names(sp.obj))) stop("names.attr should be a vector of character with a length equal to the number of variable")
# Is there a Tk window already open ?
if(interactive())
{
if(!exists("GeoXp.open",envir = baseenv())||length(ls(envir=.TkRoot$env, all.names=TRUE))==2)
{
assign("GeoXp.open", TRUE, envir = baseenv())
}
else
{if(get("GeoXp.open",envir= baseenv()))
{stop("Warning : a GeoXp function is already open. Please, close Tk window before calling a new GeoXp function to avoid conflict between graphics")}
else
{assign("GeoXp.open", TRUE, envir = baseenv())}
}
}
# we propose to refind the same arguments used in first version of GeoXp
long<-coordinates(sp.obj)[,1]
lat<-coordinates(sp.obj)[,2]
dataset <- sp.obj@data[,names.var]
listvar<-sp.obj@data
listnomvar<-names.attr
# Code which was necessary in the previous version
if(is.null(carte) & class.obj=="SpatialPolygonsDataFrame") carte<-spdf2list(sp.obj)$poly
# for colors in map and new grahics
ifelse(length(col)==1, col2<-"blue", col2<-col)
col3<-"lightblue3"
# for identifyng the selected sites
ifelse(identify, label<-row.names(listvar),label<-"")
# initialisation
nointer<-FALSE
nocart<-FALSE
buble<-FALSE
z<-NULL
legmap<-NULL
legends<-list(FALSE,FALSE,"","")
labvar=c(xlab,ylab)
graphChoice <- ""
varChoice1 <- ""
varChoice2 <- ""
choix <- ""
listgraph <- c("Histogram","Barplot","Scatterplot")
if(names.arg[1]=="") names.arg <- 1:clustnum
obs<-vector(mode = "logical", length = length(long))
# Méthodes de classification
if(length(type)==0)
{ifelse(method[1]=="kmeans",type<-"Hartigan-Wong", type <-"ward")}
# Réduction de la matrice des données
if(scale && class(dataset)!="dist") dataset<-scale(dataset)
# Etude des différentes possibilités
if(class(dataset)!="dist")
{if(method[1]=="hclust") dataset<-dist(dataset)}
else
{if(method[1]=="kmeans") dataset<-as.matrix(dataset)}
# classification
if(method[1]=="kmeans")
{
num.graph <- 4
ifelse(length(centers)==0,res <- kmeans(dataset,clustnum,algorithm=type),
res <- kmeans(dataset,centers,algorithm=type))
vectclass <- res$cluster
}
else
{
num.graph <- 5
res <- hclust(dataset,method=type)
vectclass <- as.vector(cutree(res,k=clustnum))
}
# Transformation de data.frame en matrix
if((length(listvar)>0) && (dim(as.matrix(listvar))[2]==1)) listvar<-as.matrix(listvar)
# Windows device
if(!(2%in%dev.list())) dev.new()
if(!(3%in%dev.list())) dev.new()
if(method[1]=="hclust")
{if(!(4%in%dev.list())) dev.new()}
####################################################
# sélection d'un point
####################################################
pointfunc<-function()
{
quit <- FALSE
dev.set(2)
title("ACTIVE DEVICE", cex.main = 0.8, font.main = 3, col.main='red')
title(sub = "To stop selection, click on the right button of the mouse and stop (for MAC, ESC)", cex.sub = 0.8, font.sub = 3,col.sub='red')
while(!quit)
{
#sélection des points
dev.set(2)
loc<-locator(1)
if(is.null(loc))
{
quit<-TRUE
carte(long=long, lat=lat,buble=buble,cbuble=z,criteria=criteria,nointer=nointer,obs=obs,
lablong=lablong, lablat=lablat, label=label, symbol=pch,carte=carte,nocart=nocart,
method="Cluster",classe=vectclass,couleurs=col2,legmap=legmap,legends=legends,labmod=names.arg,
cex.lab=cex.lab,axis=axes)
next
}
obs<<-selectmap(var1=long,var2=lat,obs=obs,Xpoly=loc[1], Ypoly=loc[2], method="point")
# graphiques
carte(long=long, lat=lat,buble=buble,cbuble=z,criteria=criteria,nointer=nointer,obs=obs,
lablong=lablong, lablat=lablat, label=label, symbol=pch,carte=carte,nocart=nocart,
method="Cluster",classe=vectclass,couleurs=col2,legmap=legmap,legends=legends,labmod=names.arg,
cex.lab=cex.lab,axis=axes)
title("ACTIVE DEVICE", cex.main = 0.8, font.main = 3, col.main='red')
title(sub = "To stop selection, click on the right button of the mouse and stop (for MAC, ESC)", cex.sub = 0.8, font.sub = 3,col.sub='red')
graphique(var1=vectclass, obs=obs, num=3,graph="Barplot", labvar=labvar, symbol=pch,labmod=names.arg,couleurs=col);
if ((graphChoice != "") && (varChoice1 != "") && (length(dev.list()) > 2))
{
graphique(var1=listvar[,which(listnomvar == varChoice1)], var2=listvar[,which(listnomvar == varChoice2)],
obs=obs, num=num.graph, graph=graphChoice, couleurs=col3, labvar=c(varChoice1,varChoice2))
}
}
}
####################################################
# sélection d'un polygone
####################################################
polyfunc<-function()
{
polyX <- NULL
polyY <- NULL
quit <- FALSE
dev.set(2)
title("ACTIVE DEVICE", cex.main = 0.8, font.main = 3, col.main='red')
title(sub = "To stop selection, click on the right button of the mouse and stop (for MAC, ESC)", cex.sub = 0.8, font.sub = 3,col.sub='red')
while(!quit)
{
dev.set(2)
loc<-locator(1)
if(is.null(loc))
{
quit<-TRUE
next
}
polyX <- c(polyX, loc[1])
polyY <- c(polyY, loc[2])
lines(polyX,polyY)
}
polyX <- c(polyX, polyX[1])
polyY <- c(polyY, polyY[1])
if (length(polyX)>0)
{
lines(polyX,polyY)
obs <<- selectmap(var1=long, var2=lat, obs=obs, Xpoly=polyX, Ypoly=polyY, method="poly")
#graphiques
carte(long=long, lat=lat,buble=buble,cbuble=z,criteria=criteria,nointer=nointer,obs=obs,
lablong=lablong, lablat=lablat, label=label, symbol=pch,couleurs=col2,carte=carte,nocart=nocart,
method="Cluster",classe=vectclass,legmap=legmap,legends=legends,labmod=names.arg,axis=axes,cex.lab=cex.lab)
graphique(var1=vectclass, obs=obs, num=3,graph="Barplot", labvar=labvar, symbol=pch,labmod=names.arg,
couleurs=col)
if ((graphChoice != "") && (varChoice1 != "") && (length(dev.list()) > 2))
{
graphique(var1=listvar[,which(listnomvar == varChoice1)], var2=listvar[,which(listnomvar == varChoice2)],
obs=obs, num=num.graph, graph=graphChoice, couleurs=col3, labvar=c(varChoice1,varChoice2))
}
}
}
####################################################
# sélection d'une barre sur le diagramme
####################################################
barfunc<-function()
{
SGfunc()
quit <- FALSE
dev.set(3)
title("ACTIVE DEVICE", cex.main = 0.8, font.main = 3, col.main='red')
title(sub = "To stop selection, click on the right button of the mouse and stop (for MAC, ESC)", cex.sub = 0.8, font.sub = 3,col.sub='red')
while(!quit)
{
dev.set(3)
loc<-locator(1)
if(is.null(loc))
{
quit<-TRUE
graphique(var1=vectclass, obs=obs, num=3,graph="Barplot", labvar=labvar, symbol=pch,labmod=names.arg,
couleurs=col)
next
}
obs<<-selectstat(var1=as.vector(vectclass),obs=obs,Xpoly=loc[1], Ypoly=loc[2],method="Barplot");
# graphiques
graphique(var1=vectclass, obs=obs, num=3,graph="Barplot", labvar=labvar, symbol=pch,labmod=names.arg,
couleurs=col)
title("ACTIVE DEVICE", cex.main = 0.8, font.main = 3, col.main='red')
title(sub = "To stop selection, click on the right button of the mouse and stop (for MAC, ESC)", cex.sub = 0.8, font.sub = 3,col.sub='red')
carte(long=long, lat=lat,buble=buble,cbuble=z,criteria=criteria,nointer=nointer,obs=obs,
lablong=lablong, lablat=lablat, label=label,cex.lab=cex.lab, symbol=pch,carte=carte,nocart=nocart,couleurs=col2,
method="Cluster",classe=vectclass,legmap=legmap,legends=legends,labmod=names.arg,axis=axes)
if ((graphChoice != "") && (varChoice1 != "") && (length(dev.list()) > 2))
{
graphique(var1=listvar[,which(listnomvar == varChoice1)], var2=listvar[,which(listnomvar == varChoice2)],
obs=obs, num=num.graph, graph=graphChoice, couleurs=col3, labvar=c(varChoice1,varChoice2))
}
}
}
####################################################
# choix d'un autre graphique
####################################################
graphfunc <- function()
{
if ((length(listvar) != 0) && (length(listnomvar) != 0))
{
choix <<- selectgraph(listnomvar,listgraph)
varChoice1 <<- choix$varChoice1
varChoice2 <<- choix$varChoice2
graphChoice <<- choix$graphChoice
if ((graphChoice != "") && (varChoice1 != ""))
{
if(method[1]=="kmeans")
{if(!(4%in%dev.list())) dev.new()}
else
{if(!(5%in%dev.list())) dev.new()}
graphique(var1=listvar[,which(listnomvar == varChoice1)], var2=listvar[,which(listnomvar == varChoice2)],
obs=obs, num=num.graph, graph=graphChoice, couleurs=col3, labvar=c(varChoice1,varChoice2))
}
else
{
tkmessageBox(message="You must choose a variable",icon="warning",type="ok")
}
}
else
{
tkmessageBox(message="You must give listvar and listnomvar in input",icon="warning",type="ok")
}
}
####################################################
# contour des unités spatiales
####################################################
cartfunc <- function()
{
if (length(carte) != 0)
{
ifelse(!nocart,nocart<<-TRUE,nocart<<-FALSE)
carte(long=long, lat=lat,buble=buble,cbuble=z,criteria=criteria,nointer=nointer,obs=obs,
lablong=lablong, lablat=lablat, label=label, cex.lab=cex.lab, symbol=pch,couleurs=col2,carte=carte,
nocart=nocart, method="Cluster",classe=vectclass,legmap=legmap,legends=legends,labmod=names.arg,axis=axes)
}
else
{
tkmessageBox(message="Spatial contours have not been given",icon="warning",type="ok")
}
}
####################################################
# rafraichissement des graphiques
####################################################
SGfunc<-function()
{
obs<<-vector(mode = "logical", length = length(long));
carte(long=long, lat=lat,buble=buble,cbuble=z,criteria=criteria,nointer=nointer,obs=obs,
lablong=lablong, lablat=lablat, label=label,cex.lab=cex.lab, symbol=pch,carte=carte,nocart=nocart,
couleurs=col2,method="Cluster",classe=vectclass,legmap=legmap,legends=legends,labmod=names.arg,axis=axes)
graphique(var1=vectclass, obs=obs, num=3, graph="Barplot", labvar=labvar, symbol=pch,labmod=names.arg,couleurs=col)
if ((graphChoice != "") && (varChoice1 != "") && (length(dev.list()) > 2))
{
graphique(var1=listvar[,which(listnomvar == varChoice1)], var2=listvar[,which(listnomvar == varChoice2)],
obs=obs, num=num.graph, graph=graphChoice, couleurs=col3, labvar=c(varChoice1,varChoice2))
}
}
####################################################
# quitter l'application
####################################################
quitfunc<-function()
{
#tclvalue(fin)<<-TRUE
tkdestroy(tt)
assign("GeoXp.open", FALSE, envir = baseenv())
# assign("obs", row.names(sp.obj)[obs], envir = .GlobalEnv)
}
quitfunc2<-function()
{
#tclvalue(fin)<<-TRUE
tkdestroy(tt)
assign("GeoXp.open", FALSE, envir = baseenv())
print("Results have saved in last.select object")
res<-list(obs=which(obs),vectclass=vectclass)
assign("last.select", res, envir = envir)
}
####################################################
# Open a no interactive selection
####################################################
fnointer<-function()
{
if (length(criteria) != 0)
{
ifelse(!nointer,nointer<<-TRUE,nointer<<-FALSE)
carte(long=long, lat=lat,buble=buble,cbuble=z,criteria=criteria,nointer=nointer,obs=obs,
lablong=lablong, lablat=lablat, label=label,cex.lab=cex.lab, symbol=pch,carte=carte,nocart=nocart,
couleurs=col2,method="Cluster",classe=vectclass,legmap=legmap,legends=legends,labmod=names.arg,axis=axes)
}
else
{
tkmessageBox(message="Criteria has not been given",icon="warning",type="ok")
}
}
####################################################
# Bubble
####################################################
fbubble<-function()
{
res2<-choix.bubble(buble,listvar,listnomvar,legends)
buble <<- res2$buble
legends <<- res2$legends
z <<- res2$z
legmap <<- res2$legmap
carte(long=long, lat=lat,buble=buble,cbuble=z,criteria=criteria,nointer=nointer,obs=obs,
lablong=lablong, lablat=lablat, label=label,cex.lab=cex.lab, symbol=pch,carte=carte,nocart=nocart,
couleurs=col2,method="Cluster",classe=vectclass,legmap=legmap,legends=legends,labmod=names.arg,axis=axes)
}
####################################################
# Représentation graphique
####################################################
carte(long=long, lat=lat,buble=buble,cbuble=z,criteria=criteria,nointer=nointer,obs=obs,
lablong=lablong, lablat=lablat, label=label,cex.lab=cex.lab, symbol=pch,carte=carte,nocart=nocart,
couleurs=col2,method="Cluster",classe=vectclass,legmap=legmap,legends=legends,labmod=names.arg,axis=axes)
graphique(var1=as.vector(vectclass), obs=obs, num=3, graph="Barplot", labvar=labvar, symbol=pch,
labmod=names.arg,couleurs=col)
if(method[1]=="hclust")
{dev.set(4)
plot(res)
}
####################################################
# création de la boite de dialogue to create legens
####################################################
if(interactive())
{
OnOK <- function()
{
tkdestroy(tt1)
msg <- paste("Click on the map to indicate the location of the upper left corner of the legend box")
tkmessageBox(message=msg)
dev.set(2)
loc <- locator(1)
loc$name <- "Cluster"
legends<<-list(legends[[1]],TRUE,legends[[3]],loc)
carte(long=long, lat=lat,buble=buble,cbuble=z,criteria=criteria,nointer=nointer,obs=obs,
lablong=lablong, lablat=lablat, label=label,cex.lab=cex.lab, symbol=pch,carte=carte,nocart=nocart,
couleurs=col2,method="Cluster",classe=vectclass,legmap=legmap,legends=legends,labmod=names.arg,axis=axes)
graphique(var1=as.vector(vectclass), obs=obs, num=3, graph="Barplot", labvar=labvar, symbol=pch,
labmod=names.arg,couleurs=col)
}
OnOK2 <- function()
{
legends<<-list(legends[[1]],FALSE,legends[[3]],"")
tkdestroy(tt1)
carte(long=long, lat=lat,buble=buble,cbuble=z,criteria=criteria,nointer=nointer,obs=obs,
lablong=lablong, lablat=lablat, label=label,cex.lab=cex.lab, symbol=pch,carte=carte,nocart=nocart,
couleurs=col2,method="Cluster",classe=vectclass,legmap=legmap,legends=legends,labmod=names.arg,axis=axes)
graphique(var1=as.vector(vectclass), obs=obs, num=3, graph="Barplot", labvar=labvar,
symbol=pch,labmod=names.arg,couleurs=col)
}
if(length(col)==length(levels(as.factor(vectclass)))||length(pch)==length(levels(as.factor(vectclass))))
{
tt1<-tktoplevel()
labelText12 <- tclVar("Do you want a legend for factors")
label12 <- tklabel(tt1,justify = "center", wraplength = "3i", text=tclvalue(labelText12))
tkconfigure(label12, textvariable=labelText12)
tkgrid(label12,columnspan=2)
point.but <- tkbutton(tt1, text=" Yes ", command=OnOK)
poly.but <- tkbutton(tt1, text=" No ", command=OnOK2)
tkgrid(point.but, poly.but)
tkgrid(tklabel(tt1,text=" "))
tkfocus(tt1)
}
}
####################################################
# création de la boite de dialogue
####################################################
if(interactive())
{
fontheading<-tkfont.create(family="times",size=14,weight="bold")
tt <- tktoplevel()
tkwm.title(tt, "clustermap")
frame1a <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
tkpack(tklabel(frame1a, text = "Interactive selection", font = "Times 14",
foreground = "blue", background = "white"))
tkpack(tklabel(frame1a, text = "Work on the map", font = "Times 12",
foreground = "darkred", background = "white"))
point.but <- tkbutton(frame1a, text="Selection by point", command=pointfunc);
poly.but <- tkbutton(frame1a, text="Selection by polygon ", command=polyfunc);
tkpack(point.but, poly.but, side = "left", expand = "TRUE",
fill = "x")
tkpack(frame1a, expand = "TRUE", fill = "x")
frame1c <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
tkpack(tklabel(frame1c, text = "Work on the bar plot", font = "Times 12",
foreground = "darkred", background = "white"))
barre.but <- tkbutton(frame1c, text=" Bar ", command=barfunc);
tkpack(barre.but, side = "left", expand = "TRUE", fill = "x")
tkpack(frame1c, expand = "TRUE", fill = "x")
frame1b <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
nettoy.but <- tkbutton(frame1b, text=" Reset selection " , command=SGfunc);
tkpack(nettoy.but, side = "left", expand = "TRUE", fill = "x")
tkpack(frame1b, expand = "TRUE", fill = "x")
frame2 <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
tkpack(tklabel(frame2, text = "Options", font = "Times 14",
foreground = "blue", background = "white"))
tkpack(tklabel(frame2, text = "Spatial contours", font = "Times 11",
foreground = "darkred", background = "white"),tklabel(frame2, text = "Preselected sites", font = "Times 11",
foreground = "darkred", background = "white"), side = "left", fill="x",expand = "TRUE")
tkpack(frame2, expand = "TRUE", fill = "x")
frame2b <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
nocou1.but <- tkbutton(frame2b, text="On/Off", command=cartfunc)
noint1.but <- tkbutton(frame2b, text="On/Off", command=fnointer)
tkpack(nocou1.but,noint1.but, side = "left", expand = "TRUE", fill = "x")
tkpack(frame2b, expand = "TRUE", fill = "x")
frame2c <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
tkpack(tklabel(frame2c, text = "Bubbles", font = "Times 11",
foreground = "darkred", background = "white"),tklabel(frame2c, text = "Additional graph", font = "Times 11",
foreground = "darkred", background = "white"), side = "left", fill="x",expand = "TRUE")
tkpack(frame2c, expand = "TRUE", fill = "x")
frame2d <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
bubble.but <- tkbutton(frame2d, text="On/Off", command=fbubble)
autre.but <- tkbutton(frame2d, text=" OK " , command=graphfunc)
tkpack(bubble.but,autre.but, side = "left", expand = "TRUE", fill = "x")
tkpack(frame2d, expand = "TRUE", fill = "x")
frame3 <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
tkpack(tklabel(frame3, text = "Exit", font = "Times 14",
foreground = "blue", background = "white"))
quit.but <- tkbutton(frame3, text="Save results", command=quitfunc2);
quit.but2 <- tkbutton(frame3, text="Exit without saving", command=quitfunc)
tkpack(quit.but, quit.but2, side = "left", expand = "TRUE",
fill = "x")
tkpack(frame3, expand = "TRUE", fill = "x")
}
####################################################
# Fin
####################################################
return(invisible())
}
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