boxplotmap <- function(sf.obj, name.var, criteria = NULL, carte = NULL, identify = NULL,
cex.lab = 0.8, pch = 16, col = "lightblue3",
xlab = "", ylab = "", axes = FALSE, lablong = "", lablat = "") {
###################################################
########## COMMON to ALL FUNCTIONS in GeoXp
envir <- globalenv()
# Verification of the Spatial Object sf.obj
class.obj <- class(sf.obj)[1]
if(class.obj != "sf")
stop("sf.obj may be a sf object")
if(!(name.var %in% names(sf.obj)))
stop("name.var is not included in the sf object")
# we propose to refind the same arguments used in first version of GeoXp
if (st_geometry_type(sf.obj, by_geometry = F) %in% c("POINT"))
my_coords <- st_coordinates(st_geometry(sf.obj))
else
my_coords <- st_coordinates(st_point_on_surface(st_geometry(sf.obj)))
long <- my_coords[, 1]
lat <- my_coords[, 2]
listvar <- as.data.frame(st_drop_geometry(sf.obj))
listnomvar <- colnames(listvar)
# for identifying the selected sites
if (!is.null(identify) && identify %in% colnames(sf.obj))
label <- sf.obj[[identify]]
else
label <- ""
nointer <- FALSE
nocart <- FALSE
buble <- FALSE
z <- NULL
legmap <- NULL
legends <- list(FALSE, FALSE, "", "")
labvar <- c(xlab, ylab)
graphChoice <- ""
varChoice1 <- ""
varChoice2 <- ""
choix <- ""
method <- ""
listgraph <- c("Histogram", "Barplot", "Scatterplot")
# Is there a Tk window already open ?
if (interactive()) {
if (!exists("GeoXp.open", envir = envir) ||
length(ls(envir = .TkRoot$env, all.names = TRUE)) == 2) {
assign("GeoXp.open", TRUE, envir = envir)
} else {
if (get("GeoXp.open", envir = envir)) {
stop(
"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 = envir)
}
}
}
# Windows device
if(length(dev.list()) == 0 & options("device") == "RStudioGD")
dev.new()
# for graphic
dev.new(noRStudioGD = FALSE)
num_graph <- dev.list()[length(dev.list())]
# for map
dev.new(noRStudioGD = FALSE)
num_carte <- dev.list()[length(dev.list())]
# number of devices
num_supp <- NA
#####################################################
##### Arguments proper to each function
var <- sf.obj[[name.var]]
obs <- vector(mode = "logical", length = length(long))
# verify the type of the main variable
if(!(is.integer(var) || is.double(var)))
stop("the variable name.var should be a numeric variable")
# if add a graphic barplot
labmod <- ""
# if colors
col2 <- "blue"
col3 <- col[1]
pch2 <- pch[1]
####################################################
# selection d'une partie du boxplot
####################################################
boxfunc<-function() {
quit <- FALSE
dev.set(num_graph)
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 or use ESC",
cex.sub = 0.8, font.sub = 3, col.sub = "red")
while (!quit) {
dev.set(num_graph)
loc <- locator(1)
if (is.null(loc)) {
quit<-TRUE
graphique(var1 = var, obs = obs, num = num_graph,
graph = "Boxplot", labvar = labvar,
couleurs = col, symbol = pch)
next
}
obs <<- selectstat(var1 = var, obs = obs,
Xpoly = loc[1], Ypoly = loc[2],
method = "Boxplot")
# graphiques
graphique(var1 = var, obs = obs, num = num_graph,
graph = "Boxplot", labvar = labvar,
couleurs = col, symbol = pch)
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 or use ESC",
cex.sub = 0.8, font.sub = 3, col.sub = "red")
carte(long = long, lat = lat, obs = obs, sf.obj = sf.obj, num = num_carte,
buble = buble, cbuble = z, criteria = criteria, nointer = nointer, label = label,
symbol = pch2, couleurs = col2, carte = carte, nocart = nocart, legmap = legmap,
legends = legends, axis = axes, labmod = labmod, lablong = lablong, lablat = lablat,
cex.lab = cex.lab, method = method, classe = listvar[, which(listnomvar == varChoice1)])
# Remarque : s'il y a tous ces If, c'est pour pr?voir de rajoutter un barplot avec options de couleurs
# sur la carte
if ((graphChoice != "") && (varChoice1 != "") && (length(dev.list()) > 2))
graphique(var1 = listvar[, which(listnomvar == varChoice1)],
var2 = listvar[,which(listnomvar == varChoice2)],
obs = obs, num = num_supp, graph = graphChoice, couleurs = col3,
symbol = pch, labvar = c(varChoice1, varChoice2))
}
}
####################################################
# contour des unites spatiales
####################################################
cartfunc <- function() {
if (length(carte) != 0) {
nocart <<- !nocart
carte(long = long, lat = lat, obs = obs, sf.obj = sf.obj, num = num_carte,
buble = buble, cbuble = z, criteria = criteria, nointer = nointer, label = label,
symbol = pch2, couleurs = col2, carte = carte, nocart = nocart, legmap = legmap,
legends = legends, axis = axes, labmod = labmod, lablong = lablong, lablat = lablat,
cex.lab = cex.lab, method = method, classe = listvar[, which(listnomvar == varChoice1)])
} 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))
# graphiques
graphique(var1 = var, obs = obs, num = num_graph,
graph = "Boxplot", labvar = labvar,
couleurs = col, symbol = pch)
carte(long = long, lat = lat, obs = obs, sf.obj = sf.obj, num = num_carte,
buble = buble, cbuble = z, criteria = criteria, nointer = nointer, label = label,
symbol = pch2, couleurs = col2, carte = carte, nocart = nocart, legmap = legmap,
legends = legends, axis = axes, labmod = labmod, lablong = lablong, lablat = lablat,
cex.lab = cex.lab, method = method, classe = listvar[, which(listnomvar == varChoice1)])
# Remarque : s'il y a tous ces If, c'est pour prevoir de rajoutter un barplot avec options de couleurs
# sur la carte
if ((graphChoice != "") && (varChoice1 != "") && (length(dev.list()) > 2)) {
graphique(var1 = listvar[, which(listnomvar == varChoice1)],
var2 = listvar[,which(listnomvar == varChoice2)],
obs = obs, num = num_supp, graph = graphChoice, couleurs = col3,
symbol = pch, 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 (((graphChoice == "Histogram") && (!is.numeric(listvar[,which(listnomvar == varChoice1)]))) ||
((graphChoice == "Scatterplot") && ((!is.numeric(listvar[,which(listnomvar == varChoice1)])) ||
(!is.numeric(listvar[,which(listnomvar == varChoice2)]))))) {
tkmessageBox(message = "Variables choosed are not in a good format",
icon = "warning", type = "ok")
} else {
res1 <- choix.couleur(graphChoice, listvar, listnomvar, varChoice1,
legends, col, pch, spdf = F)
method <<- res1$method
col2 <<- res1$col2
col3 <<- res1$col3
pch2 <<- res1$pch2
legends <<- res1$legends
labmod <<- res1$labmod
if(is.na(num_supp)) {
dev.new(noRStudioGD = FALSE)
num_supp <<- dev.list()[length(dev.list())]
}
graphique(var1 = listvar[, which(listnomvar == varChoice1)],
var2 = listvar[, which(listnomvar == varChoice2)],
obs = obs, num = num_supp, graph = graphChoice, couleurs = col3,
symbol = pch, labvar = c(varChoice1, varChoice2))
carte(long = long, lat = lat, obs = obs, sf.obj = sf.obj, num = num_carte,
buble = buble, cbuble = z, criteria = criteria, nointer = nointer, label = label,
symbol = pch2, couleurs = col2, carte = carte, nocart = nocart, legmap = legmap,
legends = legends, axis = axes, labmod = labmod, lablong = lablong, lablat = lablat,
cex.lab = cex.lab, method = method, classe = listvar[, which(listnomvar == varChoice1)])
}
}
} else {
tkmessageBox(message="Variables (listvar) and their names (listnomvar) must have been given",
icon = "warning", type = "ok")
}
}
####################################################
# quitter l'application
####################################################
quitfunc <- function() {
tkdestroy(tt)
assign("GeoXp.open", FALSE, envir = envir)
dev.off(num_graph)
dev.off(num_carte)
if (!is.na(num_supp))
dev.off(num_supp)
}
quitfunc2 <- function() {
fig_save <- "fig_GeoXp.pdf"
map_save <- "map_GeoXp.pdf"
k <- 1
while(file.exists(fig_save)) {
fig_save <- paste("fig_GeoXp", "_", k, ".pdf", sep = "")
k <- k + 1
}
pdf(fig_save)
graphique(var1 = var, obs = obs, num = dev.list()[length(dev.list())],
graph = "Boxplot", labvar = labvar,
couleurs = col, symbol = pch)
dev.off()
k <- 1
while(file.exists(map_save)) {
map_save <- paste("map_GeoXp", "_", k, ".pdf", sep = "")
k <- k + 1
}
pdf(map_save)
carte(long = long, lat = lat, obs = obs, sf.obj = sf.obj, num = dev.list()[length(dev.list())],
buble = buble, cbuble = z, criteria = criteria, nointer = nointer, label = label,
symbol = pch2, couleurs = col2, carte = carte, nocart = nocart, legmap = legmap,
legends = legends, axis = axes, labmod = labmod, lablong = lablong, lablat = lablat,
cex.lab = cex.lab, method = method, classe = listvar[, which(listnomvar == varChoice1)])
dev.off()
if(!is.na(num_supp)) {
fig_supp <- "fig_supp_GeoXp.pdf"
k <- 1
while(file.exists(fig_supp)) {
fig_supp <- paste("fig_supp_GeoXp", "_", k, ".pdf", sep = "")
k <- k + 1
}
pdf(fig_supp)
graphique(var1 = listvar[, which(listnomvar == varChoice1)],
var2 = listvar[, which(listnomvar == varChoice2)],
obs = obs, num = dev.list()[length(dev.list())], graph = graphChoice, couleurs = col3,
symbol = pch, labvar = c(varChoice1, varChoice2))
dev.off()
}
tkdestroy(tt)
assign("GeoXp.open", FALSE, envir = envir)
cat("Results have been saved in last.select object \n")
cat("Map has been saved in", map_save, "\n")
cat("Figure has been saved in", fig_save, "\n")
if(!is.na(num_supp))
cat("Supplemental figure has been saved in", fig_supp, "\n")
assign("last.select", which(obs), envir = envir)
dev.off(num_carte)
dev.off(num_graph)
if(!is.na(num_supp))
dev.off(num_supp)
}
####################################################
# Open a no interactive selection
####################################################
fnointer <- function() {
if (length(criteria) != 0) {
nointer <<- !nointer
carte(long = long, lat = lat, obs = obs, sf.obj = sf.obj, num = num_carte,
buble = buble, cbuble = z, criteria = criteria, nointer = nointer, label = label,
symbol = pch2, couleurs = col2, carte = carte, nocart = nocart, legmap = legmap,
legends = legends, axis = axes, labmod = labmod, lablong = lablong, lablat = lablat,
cex.lab = cex.lab, method = method, classe = listvar[, which(listnomvar == varChoice1)])
} else {
tkmessageBox(message = "Criteria has not been given",
icon = "warning", type = "ok")
}
}
####################################################
# Bubble
####################################################
fbubble<-function() {
res2 <- choix.bubble(buble, listvar, listnomvar, legends, num_graph, num_carte)
buble <<- res2$buble
legends <<- res2$legends
z <<- res2$z
legmap <<- res2$legmap
carte(long = long, lat = lat, obs = obs, sf.obj = sf.obj, num = num_carte,
buble = buble, cbuble = z, criteria = criteria, nointer = nointer, label = label,
symbol = pch2, couleurs = col2, carte = carte, nocart = nocart, legmap = legmap,
legends = legends, axis = axes, labmod = labmod, lablong = lablong, lablat = lablat,
cex.lab = cex.lab, method = method, classe = listvar[, which(listnomvar == varChoice1)])
}
####################################################
# Representation des graphiques
####################################################
carte(long = long, lat = lat, obs = obs, sf.obj = sf.obj, num = num_carte,
buble = buble, cbuble = z, criteria = criteria, nointer = nointer, label = label,
symbol = pch2, couleurs = col2, carte = carte, nocart = nocart, legmap = legmap,
legends = legends, axis = axes, labmod = labmod, lablong = lablong, lablat = lablat,
cex.lab = cex.lab, method = method, classe = listvar[, which(listnomvar == varChoice1)])
graphique(var1 = var, obs = obs, num = num_graph,
graph = "Boxplot", labvar = labvar,
couleurs = col, symbol = pch)
####################################################
# cr?ation de la boite de dialogue
####################################################
if (interactive()) {
fontheading <- tkfont.create(family = "times", size = 14,
weight = "bold")
tt <- tktoplevel()
tkwm.title(tt, "boxplotmap")
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 boxplot", font = "Times 12",
foreground = "darkred", background = "white"))
barre.but <- tkbutton(frame1a, text="Boxplot", command=boxfunc);
tkpack(barre.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"), 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")
}
####################################################
return(invisible())
}
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