R/variocloudmap.R

In GeoXp: Interactive exploratory spatial data analysis

`variocloudmap` <- function(sp.obj, name.var, bin=NULL, quantiles=TRUE,
names.attr=names(sp.obj), criteria=NULL, carte=NULL, identify=FALSE, cex.lab=0.8,
pch=16, col="lightblue3", xlab="", ylab="", axes=FALSE, lablong="", lablat="",
xlim=NULL, ylim=NULL)
{
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(name.var) & is.na(match(as.character(name.var),names(sp.obj)))) stop("name.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")

# we propose to refind the same arguments used in first version of GeoXp
long<-coordinates(sp.obj)[,1]
lat<-coordinates(sp.obj)[,2]

var<-sp.obj@data[,name.var]

# verify the type of the main variable
if(!(is.integer(var) || is.double(var))) stop("the variable name.var should be a numeric variable")


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 identifyng the selected sites
ifelse(identify, label<-row.names(listvar),label<-"")

# initialisation
  nointer<-FALSE
  nocart<-FALSE
  buble<-FALSE
  legends<-list(FALSE,FALSE,"","")
  z<-NULL 
  legmap<-NULL
  inout<-NULL
  labvar<-c(xlab,ylab)
    
  opt1<-1
  opt2<-1
  
  angle<-0
  names.slide="Alpha Quantile Value"
  obs <- matrix(FALSE, nrow = length(long), ncol = length(long))

  directionnel<-FALSE
  
  
# Windows device
if(!(2%in%dev.list())) dev.new()
if(!(3%in%dev.list())) dev.new()


# Transformation data.frame en matrix
if((length(listvar)>0)&&(dim(as.matrix(listvar))[2]==1)) listvar<-as.matrix(listvar)


####################################################
# calcul des matrices diff et dist
####################################################

  long1 <- matrix(rep(t(long), length(long)), ncol = dim(t(long))[2],byrow = FALSE)
  long2 <- matrix(rep(t(long), length(long)), ncol = dim(t(long))[2],byrow = TRUE)
    
  lat1 <- matrix(rep(t(lat), length(lat)), ncol = dim(t(lat))[2],byrow = FALSE)
  lat2 <- matrix(rep(t(lat), length(lat)), ncol = dim(t(lat))[2],byrow = TRUE)
  
  v1 <- matrix(rep(t(var), length(var)), ncol = dim(t(var))[2],byrow = FALSE)
  v2 <- matrix(rep(t(var), length(var)), ncol = dim(t(var))[2],byrow = TRUE)

 theta <- matrix(0, nrow = length(long), ncol = length(long))
 numer <- lat2 - lat1
 denom <- long2 - long1
   
  theta[which(denom == 0,arr.ind=TRUE)] <- pi/2
  theta[which(denom != 0,arr.ind=TRUE)] <- atan(numer[which(denom != 0,arr.ind=TRUE)]/denom[which(denom != 0,arr.ind=TRUE)])

  theta[which(theta < 0)] <- theta[which(theta < 0)] + pi

  dist <- sqrt((long1 - long2)^2 + (lat1 - lat2)^2)
  dif <-  (v1 - v2)^2/2
  dif2 <-  (abs(v1 - v2))^(1/2)


####################################################
# choix des bornes des réglettes (inspiré de la documentation de Matlab)
####################################################

#   v4 <- sort(dist)
#   v4 <- as.vector(v4)
#   z <- seq(1, max(v4), by = (max(v4)/3500))
#   z <- round(z)
#   z1 <- z[2:length(z)] - z[1:(length(z) - 1)]
#   h <- mean(z1)
#   p <- 1/(1 + (h^3/6))
#   p1 <- 1/(1 + (h^3/60))
#   p2 <- 1/(1 + (h^3/0.6))
#   alpha <- (1 - p)/p
#   borne1 <- (1 - p1)/p1
#   borne2 <- (1 - p2)/p2

borne1=0.01
borne2=0.99
alpha=0.5
####################################################
# sélection d'un point sur le variocloud
####################################################

    pointfunc <- function() 
     {
        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 = dist, var2 = dif, var3=dif2, obs = obs,opt1=opt1,opt2=opt2, num = 3, 
               graph = "Variocloud", labvar = labvar, symbol = pch, couleurs=col, quantiles = quantiles, 
               alpha1 = alpha, bin=bin, xlim=xlim, ylim=ylim)
                next
            }
     obs <<- selectstat(var1 = dist, var2 = dif, obs = obs,Xpoly = loc[1], Ypoly = loc[2], 
     method = "Variopoint",long = long, lat = lat)
     
     graphique(var1 = dist, var2 = dif, var3=dif2, obs = obs,opt1=opt1,opt2=opt2, num = 3, 
     graph = "Variocloud", labvar = labvar, symbol = pch, couleurs=col, quantiles = quantiles, 
     alpha1 = alpha, bin=bin, xlim=xlim, ylim=ylim)
     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, obs = obs, lablong = lablong,lablat = lablat, 
     label = label,buble=buble,criteria=criteria,nointer=nointer,cbuble=z,carte=carte,nocart=nocart, 
     cex.lab=cex.lab, method = "Variocloud",axis=axes,legmap=legmap,legends=legends)

     }
}

####################################################
# sélection d'un polygone sur l'angleplot
####################################################

    polyfunc <- function() {
        quit <- FALSE
        polyX <- NULL
        polyY <- NULL
        
        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
                next
            }
            polyX <- c(polyX, loc[1])
            polyY <- c(polyY, loc[2])
           if (length(polyX)>0)
           {
            lines(polyX, polyY)
           }
        }
        polyX <- c(polyX, polyX[1])
        polyY <- c(polyY, polyY[1])

    if (length(polyX)>0)
    {
        lines(polyX, polyY)
        for (i in 1:length(long)) 
        {
            obs[, i] <<- inout(cbind(dist[, i], dif[, i]), cbind(polyX, polyY), bound = TRUE)
        }
        
     graphique(var1 = dist, var2 = dif, var3=dif2, obs = obs,opt1=opt1,opt2=opt2, num = 3, 
     graph = "Variocloud", labvar = labvar, symbol = pch, couleurs=col, quantiles = quantiles, 
     alpha1 = alpha, bin=bin, xlim=xlim, ylim=ylim)
     
     carte(long = long, lat = lat, obs = obs, lablong = lablong,lablat = lablat, 
     label = label,buble=buble,criteria=criteria,nointer=nointer,cbuble=z,carte=carte,nocart=nocart, 
     cex.lab=cex.lab, method = "Variocloud",axis=axes,legmap=legmap,legends=legends)
    }
}



####################################################
# contour des unités spatiales
####################################################
cartfunc <- function()
{
if (length(carte) != 0)
   {
    ifelse(!nocart,nocart<<-TRUE,nocart<<-FALSE)    
    carte(long = long, lat = lat, obs = obs, lablong = lablong,lablat = lablat, 
    label = label,buble=buble,criteria=criteria,nointer=nointer,cbuble=z,carte=carte,nocart=nocart, 
    cex.lab=cex.lab, method = "Variocloud",axis=axes,legmap=legmap,legends=legends)
   }
   else
   {
    tkmessageBox(message="Spatial contours have not been given",icon="warning",type="ok")    
   }
}

####################################################
# Pour le alpha 
####################################################
    refresh.code <- function(...) 
    {
     alpha <<- slider1(names.slide=names.slide, no = 1)
     graphique(var1 = dist, var2 = dif, var3=dif2, obs = obs,opt1=opt1,opt2=opt2, num = 3, 
     graph = "Variocloud", labvar = labvar, symbol = pch, couleurs=col, quantiles = quantiles, 
     alpha1 = alpha, bin=bin, xlim=xlim, ylim=ylim)
    }



####################################################
# rafraichissement des graphiques
####################################################

    SGfunc <- function() 
    {
     obs <<- matrix(FALSE, nrow = length(long), ncol = length(long))
      
     graphique(var1 = dist, var2 = dif, var3=dif2, obs = obs,opt1=opt1,opt2=opt2, num = 3, 
     graph = "Variocloud", labvar = labvar, symbol = pch, couleurs=col, quantiles = quantiles, 
     alpha1 = alpha, bin=bin, xlim=xlim, ylim=ylim)
     
     carte(long = long, lat = lat, obs = obs, lablong = lablong,lablat = lablat, 
     label = label,buble=buble,criteria=criteria,nointer=nointer,cbuble=z,carte=carte,nocart=nocart, 
     cex.lab=cex.lab, method = "Variocloud",axis=axes,legmap=legmap,legends=legends)
    }


####################################################
# 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 been saved in last.select object")
    obs[lower.tri(obs)]<-FALSE
    assign("last.select", which(obs,arr.ind=TRUE), envir = envir)
}

####################################################
# Open a no interactive selection
####################################################

fnointer<-function() 
{
 if (length(criteria) != 0)
 {
  ifelse(!nointer,nointer<<-TRUE,nointer<<-FALSE)
  carte(long = long, lat = lat, obs = obs, lablong = lablong,lablat = lablat, 
  label = label,buble=buble,criteria=criteria,nointer=nointer,cbuble=z,carte=carte,nocart=nocart, 
  cex.lab=cex.lab, method = "Variocloud",axis=axes,legmap=legmap,legends=legends)
 }
 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, obs = obs, lablong = lablong,lablat = lablat, 
     label = label,buble=buble,criteria=criteria,nointer=nointer,cbuble=z,carte=carte,nocart=nocart, 
     cex.lab=cex.lab, method = "Variocloud",axis=axes,legmap=legmap,legends=legends)
}

####################################################
# Dessin du variogramme 
####################################################

 vari<-function()
 {
  ifelse(opt1==1,opt1<<-2,opt1<<-1)
  
  graphique(var1 = dist, var2 = dif, var3=dif2, obs = obs,opt1=opt1,opt2=opt2, num = 3, 
  graph = "Variocloud", labvar = labvar, symbol = pch, couleurs=col, quantiles = quantiles, 
  alpha1 = alpha, bin=bin, xlim=xlim, ylim=ylim)    
 }

 vari2<-function()
 {
  ifelse(opt2==1,opt2<<-2,opt2<<-1)
  
  graphique(var1 = dist, var2 = dif, var3=dif2, obs = obs,opt1=opt1,opt2=opt2, num = 3, 
  graph = "Variocloud", labvar = labvar, symbol = pch, couleurs=col, quantiles = quantiles, 
  alpha1 = alpha, bin=bin, xlim=xlim, ylim=ylim)    
 }


####################################################
# Choisir angle
####################################################

choixangle <- function() 
{

 directionnel<-!directionnel
 
 if(directionnel)
  {SGfunc()
  tt1<-tktoplevel()
  Name <- tclVar("0.5")
  entry.Name <-tkentry(tt1,width="3",textvariable=Name)
  tkgrid(tklabel(tt1,text="Please enter a decimal x between 0 and 1 (angle=x.Pi)"),entry.Name)

  OnOK <- function()
   {
  	angle <<- tclvalue(Name)
   	tkdestroy(tt1)
       
    if (is.na(as.numeric(angle))||(as.numeric(angle)>1)||(as.numeric(angle)<0))
    {
     tkmessageBox(message="Sorry, but you have to choose a decimal number between 0 and 1 (exemple : 0.5)",icon="warning",type="ok");
    }
    else
    {msg <- paste("You choose",angle,"pi")
	   tkmessageBox(message=msg)
    
     dist <<- sqrt((long1 - long2)^2 + (lat1 - lat2)^2)
     dif <<-  (v1 - v2)^2
     dif2 <<-  (abs(v1 - v2))^(1/2)

    if(as.numeric(angle)<1/10)
     { dist[which((theta>as.numeric(angle)*pi+pi/10)&(theta<9*pi/10+as.numeric(angle)*pi))] <<- -10
       dif[which((theta>as.numeric(angle)*pi+pi/10)&(theta<9*pi/10+as.numeric(angle)*pi))] <<- -10
       dif2[which((theta>as.numeric(angle)*pi+pi/10)&(theta<9*pi/10+as.numeric(angle)*pi))] <<- -10
     }
       else if (as.numeric(angle)>9/10)
        { dist[which((theta>-2*pi+(as.numeric(angle)*pi+11*pi/10))&(theta<as.numeric(angle)*pi-pi/10))] <<- -10
          dif[which((theta>-2*pi+(as.numeric(angle)*pi+11*pi/10))&(theta<as.numeric(angle)*pi-pi/10))] <<- -10
          dif2[which((theta>-2*pi+(as.numeric(angle)*pi+11*pi/10))&(theta<as.numeric(angle)*pi-pi/10))] <<- -10
        }
    else
    {
     dist[which((theta>as.numeric(angle)*pi+pi/10))] <<- -10
     dist[which((theta<as.numeric(angle)*pi-pi/10))] <<- -10
     dif[which((theta>as.numeric(angle)*pi+pi/10))] <<- -10
     dif[which((theta<as.numeric(angle)*pi-pi/10))] <<- -10
     dif2[which((theta>as.numeric(angle)*pi+pi/10))] <<- -10
     dif2[which((theta<as.numeric(angle)*pi-pi/10))] <<- -10
    }
    
    graphique(var1 = dist, var2 = dif, var3=dif2, obs = obs,opt1=opt1,opt2=opt2, num = 3, 
    graph = "Variocloud", labvar = labvar, symbol = pch, couleurs=col, quantiles = quantiles, 
    alpha1 = alpha, bin=bin, xlim=xlim, ylim=ylim)    
   }
}

OK.but <-tkbutton(tt1,text="   OK   ",command=OnOK)
#tkbind(entry.Name, "<Return>",OnOK)
tkgrid(OK.but)
tkfocus(tt1)
}
else
{
     SGfunc()

     dist <<- sqrt((long1 - long2)^2 + (lat1 - lat2)^2)
     dif <<-  (v1 - v2)^2/2
     dif2 <<-  (abs(v1 - v2))^(1/2)

     graphique(var1 = dist, var2 = dif, var3=dif2, obs = obs,opt1=opt1,opt2=opt2, num = 3,
     graph = "Variocloud", labvar = labvar, symbol = pch, couleurs=col, quantiles = quantiles,
     alpha1 = alpha, bin=bin, xlim=xlim, ylim=ylim)
}

}


####################################################
# Représentation Graphique
####################################################
# Is there a Tk window already open ?
if(interactive())
{
 if(!exists("GeoXp.open",envir = baseenv())||length(ls(envir=.TkRoot$env, all.names=TRUE))==2)  # new environment
 {
   graphique(var1 = dist, var2 = dif, var3=dif2, obs = obs,opt1=opt1,opt2=opt2, num = 3, 
   graph = "Variocloud", labvar = labvar, symbol = pch, couleurs=col, quantiles = quantiles, 
   alpha1 = alpha, bin=bin, xlim=xlim, ylim=ylim)
     
   carte(long = long, lat = lat, obs = obs, lablong = lablong,lablat = lablat, 
   label = label,buble=buble,criteria=criteria,nointer=nointer,cbuble=z,carte=carte,nocart=nocart, 
   cex.lab=cex.lab, method = "Variocloud",axis=axes,legmap=legmap,legends=legends)
   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
  { graphique(var1 = dist, var2 = dif, var3=dif2, obs = obs,opt1=opt1,opt2=opt2, num = 3, 
    graph = "Variocloud", labvar = labvar, symbol = pch, couleurs=col, quantiles = quantiles, 
    alpha1 = alpha, bin=bin, xlim=xlim, ylim=ylim)
     
    carte(long = long, lat = lat, obs = obs, lablong = lablong,lablat = lablat, 
    label = label,buble=buble,criteria=criteria,nointer=nointer,cbuble=z,carte=carte,nocart=nocart, 
    cex.lab=cex.lab, method = "Variocloud",axis=axes,legmap=legmap,legends=legends)
    assign("GeoXp.open", TRUE, envir = baseenv())}
 }
}
          
####################################################
# création de la boite de dialogue
####################################################

if(interactive())
{
fontheading<-tkfont.create(family="times",size=14,weight="bold")

tt <- tktoplevel()
tkwm.title(tt, "variocloudmap")

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 graph", 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")

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"),tklabel(frame2, text = "  Bubbles    ", 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)
bubble.but <- tkbutton(frame2b, text="On/Off", command=fbubble)
tkpack(nocou1.but,noint1.but,bubble.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 = "Classic empirical semi-variogram ", font = "Times 11",
foreground = "darkred", background = "white"),tklabel(frame2c, text = "Robust empirical semi-variogram  ", 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")
vari.but <- tkbutton(frame2d, text="On/Off", command=vari)
vari2.but <- tkbutton(frame2d, text="On/Off", command=vari2)
tkpack(vari.but, vari2.but, side = "left", expand = "TRUE", fill = "x")
tkpack(frame2d, expand = "TRUE", fill = "x")

frame2e <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
tkpack(tklabel(frame2e, text = "Directional Semi-Variogram Cloud", font = "Times 11",
foreground = "darkred", background = "white"),side = "left", fill="x",expand = "TRUE")
tkpack(frame2e, expand = "TRUE", fill = "x")

frame2f <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
angle.but <- tkbutton(frame2f, text="On/Off", command=choixangle)
tkpack(angle.but, side = "left", expand = "TRUE", fill = "x")
tkpack(frame2f, expand = "TRUE", fill = "x")


if(quantiles)
{
frame1c <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")

slider1(frame1c, refresh.code, names.slide=names.slide,
        borne1, borne2, (borne2 - borne1)/100, alpha)

tkpack(frame1c, 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")
}

####################################################
return(invisible())

}