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R/plot.MCA.R
In FactoMineR: Multivariate Exploratory Data Analysis and Data Mining
plot.MCA <- function (x, axes = c(1, 2), choix=c("ind","var","quanti.sup"),
xlim = NULL, ylim = NULL, invisible = c("none","ind", "var", "ind.sup", "quali.sup", "quanti.sup"),
col.ind = "black", col.var = "red", col.quali.sup = "darkgreen",
col.ind.sup = "blue", col.quanti.sup = "blue",
label=c("all","none","ind", "var", "ind.sup", "quali.sup", "quanti.sup"), title = NULL, habillage = "none", palette=NULL,
autoLab = c("auto","yes","no"),new.plot=FALSE,select=NULL,selectMod=NULL, unselect=0.7, shadowtext=FALSE,
legend = list(bty = "y", x = "topleft"), graph.type = c("ggplot","classic"), ggoptions = NULL, ...){
label <- match.arg(label,c("all","none","ind", "var", "ind.sup", "quali.sup", "quanti.sup"),several.ok=TRUE)
choix <- match.arg(choix,c("ind","var","quanti.sup"))
graph.type <- match.arg(graph.type[1],c("ggplot","classic"))
autoLab <- match.arg(autoLab,c("auto","yes","no"))
argument <- list(...)
if (!is.null(argument[["cex"]]) & is.null(ggoptions["size"])) ggoptions["size"] <- 4*argument$cex
ggoptions_default <- list(size = 4, point.shape = 19, line.lty = 2, line.lwd = 0.5, line.color = "black", segment.lty = 1, segment.lwd = 0.5, circle.lty = 1, circle.lwd = 0.5, circle.color = "black", low.col.quanti = "blue", high.col.quanti = "red3")
if (!is.null(ggoptions[1])) ggoptions_default[names(ggoptions)] <- ggoptions[names(ggoptions)]
old.palette <- palette()
if (is.null(palette)) palette <- c("black", "red", "green3", "blue", "magenta", "darkgoldenrod","darkgray", "orange", "cyan", "violet", "lightpink", "lavender", "yellow", "darkgreen","turquoise", "lightgrey", "lightblue", "darkkhaki","darkmagenta","lightgreen", "darkolivegreen", "lightcyan", "darkorange","darkorchid", "darkred", "darksalmon", "darkseagreen","darkslateblue", "darkslategray", "darkslategrey","darkturquoise", "darkviolet", "lightgray", "lightsalmon","lightyellow", "maroon")
palette(palette) # that is necessary
if (autoLab=="yes") autoLab <- TRUE
if (autoLab=="no") autoLab <- FALSE
invisible <- match.arg(invisible,c("none","ind", "var", "ind.sup", "quali.sup", "quanti.sup"),several.ok=TRUE)
if ("none"%in%invisible) invisible <- NULL
res.mca <- x
if (!inherits(res.mca, "MCA")) stop("non convenient data")
if (is.numeric(unselect)) if ((unselect>1)|(unselect<0)) stop("unselect should be betwwen 0 and 1")
lab.x <- paste("Dim ",axes[1]," (",format(res.mca$eig[axes[1],2],nsmall=2,digits=2),"%)",sep="")
lab.y <- paste("Dim ",axes[2]," (",format(res.mca$eig[axes[2],2],nsmall=2,digits=2),"%)",sep="")
if (graph.type == "ggplot"){
theme <- theme(
axis.title = element_text(hjust = 1, size = if (is.null(argument[["cex.axis"]])) {10} else {10*argument$cex.axis},face = 2),
plot.title = element_text(hjust = 0.5, size = if (is.null(argument[["cex.main"]])) {11} else {11*argument$cex.main},face = 2),
legend.position = ifelse(legend$x %in% c("bottom","up","right","left"), legend$x, "right"),
legend.box.spacing=unit(0.1, 'cm'),legend.margin=margin()
)
}
if (choix =="ind"){
lab.ind <- lab.var <- lab.quali.sup <- lab.ind.sup <- FALSE
if(length(label)==1 && label=="all") lab.ind <- lab.var <- lab.quali.sup <- lab.ind.sup <- TRUE
if("ind" %in% label) lab.ind<-TRUE
if("var" %in% label) lab.var<-TRUE
if("quali.sup" %in% label) lab.quali.sup<-TRUE
if("ind.sup" %in% label) lab.ind.sup<-TRUE
test.invisible <- vector(length = 5)
if (!is.null(invisible)) {
test.invisible[1] <- match("ind", invisible)
test.invisible[2] <- match("var", invisible)
test.invisible[3] <- match("quanti.sup", invisible)
test.invisible[4] <- match("ind.sup", invisible)
test.invisible[5] <- match("quali.sup", invisible)
}
else test.invisible <- rep(NA, 5)
coord.var <- res.mca$var$coord[, axes]
coord.ind <- res.mca$ind$coord[, axes]
coord.ind.sup <- coord.quali.sup <- NULL
if (!is.null(res.mca$ind.sup)) coord.ind.sup <- res.mca$ind.sup$coord[, axes,drop=FALSE]
if (!is.null(res.mca$quali.sup)) coord.quali.sup <- res.mca$quali.sup$coord[, axes,drop=FALSE]
nullxlimylim <- (is.null(xlim) & is.null(ylim))
if (is.null(xlim)) {
xmin <- xmax <- 0
if(is.na(test.invisible[1])) xmin <- min(xmin, coord.ind[,1])
if(is.na(test.invisible[1])) xmax <- max(xmax, coord.ind[,1])
if(is.na(test.invisible[4])) xmin <- min(xmin, coord.ind.sup[, 1])
if(is.na(test.invisible[4])) xmax <- max(xmax, coord.ind.sup[, 1])
if(is.na(test.invisible[2])) xmin <- min(xmin, coord.var[,1])
if(is.na(test.invisible[2])) xmax <- max(xmax, coord.var[,1])
if(is.na(test.invisible[5])) xmin <- min(xmin, coord.quali.sup[, 1])
if(is.na(test.invisible[5])) xmax <- max(xmax, coord.quali.sup[, 1])
# xlim <- c(xmin, xmax) * 1.2
xlim <- c(xmin, xmax)
xlim <- (xlim-mean(xlim))*1.2 + mean(xlim)
}
if (is.null(ylim)) {
ymin <- ymax <- 0
if(is.na(test.invisible[1])) ymin <- min(ymin, coord.ind[,2])
if(is.na(test.invisible[1])) ymax <- max(ymax, coord.ind[,2])
if(is.na(test.invisible[4])) ymin <- min(ymin, coord.ind.sup[, 2])
if(is.na(test.invisible[4])) ymax <- max(ymax, coord.ind.sup[, 2])
if(is.na(test.invisible[2])) ymin <- min(ymin, coord.var[,2])
if(is.na(test.invisible[2])) ymax <- max(ymax, coord.var[,2])
if(is.na(test.invisible[5])) ymin <- min(ymin, coord.quali.sup[,2])
if(is.na(test.invisible[5])) ymax <- max(ymax, coord.quali.sup[,2])
# ylim <- c(ymin, ymax) * 1.2
ylim <- c(ymin, ymax)
ylim <- (ylim-mean(ylim))*1.2 + mean(ylim)
}
if (nullxlimylim & diff(xlim)/diff(ylim)>3) ylim <- (ylim-mean(ylim))*diff(xlim)/diff(ylim)/3 + mean(ylim)
if (nullxlimylim & diff(xlim)/diff(ylim)<1/2) xlim <- (xlim-mean(xlim))*diff(ylim)/diff(xlim)/2 + mean(xlim)
if(graph.type=="ggplot") nudge_y <- (ylim[2] - ylim[1])*0.03
selection <- selectionS <- selection2 <- selection3 <- NULL
if (!is.null(select)) {
if (mode(select)=="numeric") selection <- select
else {
if (sum(rownames(res.mca$ind$coord)%in%select)!=0) selection <- which(rownames(res.mca$ind$coord)%in%select)
else {
if (grepl("contrib",select)) selection <- (rev(order(res.mca$ind$contrib[,axes[1],drop=FALSE]*res.mca$eig[axes[1],1]+res.mca$ind$contrib[,axes[2],drop=FALSE]*res.mca$eig[axes[2],1])))[1:min(nrow(res.mca$ind$coord),sum(as.integer(unlist(strsplit(select,"contrib"))),na.rm=T))]
# if (grepl("contrib",select)) selection <- (rev(order(apply(res.mca$ind$contrib[,axes,drop=FALSE],1,sum))))[1:min(nrow(res.mca$ind$coord),sum(as.integer(unlist(strsplit(select,"contrib"))),na.rm=T))]
if (grepl("coord",select)) selection <- (rev(order(apply(res.mca$ind$coord[,axes,drop=FALSE]^2,1,sum))))[1:min(nrow(res.mca$ind$coord),sum(as.integer(unlist(strsplit(select,"coord"))),na.rm=T))]
if (grepl("cos2",select)) {
if (sum(as.numeric(unlist(strsplit(select,"cos2"))),na.rm=T)>=1) selection <- (rev(order(apply(res.mca$ind$cos2[,axes,drop=FALSE],1,sum))))[1:min(nrow(res.mca$ind$coord),sum(as.numeric(unlist(strsplit(select,"cos2"))),na.rm=T))]
else selection <- which(apply(res.mca$ind$cos2[,axes,drop=FALSE],1,sum)>sum(as.numeric(unlist(strsplit(select,"cos2"))),na.rm=T))
}
if (is.integer(select)) selection <- select
}
}
}
if (!is.null(select)&(!is.null(res.mca$call$ind.sup))) {
if (mode(select)=="numeric") selectionS <- select
else {
if (sum(rownames(res.mca$ind.sup$coord)%in%select)!=0) selectionS <- which(rownames(res.mca$ind.sup$coord)%in%select)
else {
if (grepl("contrib",select)) selectionS <- NULL
if (grepl("coord",select)) selectionS <- (rev(order(apply(res.mca$ind.sup$coord[,axes,drop=FALSE]^2,1,sum))))[1:min(nrow(res.mca$ind.sup$coord),sum(as.integer(unlist(strsplit(select,"coord"))),na.rm=T))]
if (grepl("cos2",select)) {
if (sum(as.numeric(unlist(strsplit(select,"cos2"))),na.rm=T)>=1) selectionS <- (rev(order(apply(res.mca$ind.sup$cos2[,axes,drop=FALSE],1,sum))))[1:min(nrow(res.mca$ind.sup$coord),sum(as.numeric(unlist(strsplit(select,"cos2"))),na.rm=T))]
else selectionS <- which(apply(res.mca$ind.sup$cos2[,axes,drop=FALSE],1,sum)>sum(as.numeric(unlist(strsplit(select,"cos2"))),na.rm=T))
}
if (is.integer(select)) selectionS <- select
}
}
}
if (!is.null(selectMod)) {
if (mode(selectMod)=="numeric") selection2 <- selectMod
else {
if (sum(rownames(res.mca$var$coord)%in%selectMod)+sum(rownames(res.mca$quali.sup$coord)%in%selectMod)!=0) selection2 <- which(rownames(res.mca$var$coord)%in%selectMod)
else {
if (grepl("contrib",selectMod)) selection2 <- (rev(order(res.mca$var$contrib[,axes[1],drop=FALSE]*res.mca$eig[axes[1],1]+res.mca$var$contrib[,axes[2],drop=FALSE]*res.mca$eig[axes[2],1])))[1:min(nrow(res.mca$var$coord),sum(as.integer(unlist(strsplit(selectMod,"contrib"))),na.rm=T))]
if (grepl("coord",selectMod)) selection2 <- (rev(order(apply(res.mca$var$coord[,axes,drop=FALSE]^2,1,sum))))[1:min(nrow(res.mca$var$coord),sum(as.integer(unlist(strsplit(selectMod,"coord"))),na.rm=T))]
if (grepl("cos2",selectMod)) {
if (sum(as.numeric(unlist(strsplit(selectMod,"cos2"))),na.rm=T)>=1) selection2 <- (rev(order(apply(res.mca$var$cos2[,axes],1,sum))))[1:min(nrow(res.mca$var$coord),sum(as.numeric(unlist(strsplit(selectMod,"cos2"))),na.rm=T))]
else selection2 <- which(apply(res.mca$var$cos2[,axes],1,sum)>sum(as.numeric(unlist(strsplit(selectMod,"cos2"))),na.rm=T))
}
if (grepl("v.test",selectMod)) selection2 <- union(which(abs(res.mca$var$v.test[,axes[1],drop=FALSE])>sum(as.integer(unlist(strsplit(selectMod,"v.test"))),na.rm=T)),which(abs(res.mca$var$v.test[,axes[2],drop=FALSE])>sum(as.integer(unlist(strsplit(selectMod,"v.test"))),na.rm=T)))
if (is.integer(selectMod)) selection2 <- selectMod
}
}
}
if ((!is.null(selectMod))&(!is.null(res.mca$call$quali.sup))) {
if (mode(selectMod)=="numeric") selection3 <- selectMod
else {
if (sum(rownames(res.mca$var$coord)%in%selectMod)+sum(rownames(res.mca$quali.sup$coord)%in%selectMod)!=0) selection3 <- which(rownames(res.mca$quali.sup$coord)%in%selectMod)
else {
if (grepl("contrib",selectMod)) selection3 <- NULL
if (grepl("coord",selectMod)) selection3 <- (rev(order(apply(res.mca$quali.sup$coord[,axes,drop=FALSE]^2,1,sum))))[1:min(nrow(res.mca$quali.sup$coord),sum(as.integer(unlist(strsplit(selectMod,"coord"))),na.rm=T))]
if (grepl("cos2",selectMod)) {
if (sum(as.numeric(unlist(strsplit(selectMod,"cos2"))),na.rm=T)>=1) selection3 <- (rev(order(apply(res.mca$quali.sup$cos2[,axes,drop=FALSE],1,sum))))[1:min(nrow(res.mca$quali.sup$coord),sum(as.numeric(unlist(strsplit(selectMod,"cos2"))),na.rm=T))]
else selection3 <- which(apply(res.mca$quali.sup$cos2[,axes,drop=FALSE],1,sum)>sum(as.numeric(unlist(strsplit(selectMod,"cos2"))),na.rm=T))
}
if (grepl("v.test",selectMod)) selection3 <- union(which(abs(res.mca$quali.sup$v.test[,axes[1],drop=FALSE])>sum(as.integer(unlist(strsplit(selectMod,"v.test"))),na.rm=T)),which(abs(res.mca$quali.sup$v.test[,axes[2],drop=FALSE])>sum(as.integer(unlist(strsplit(selectMod,"v.test"))),na.rm=T)))
if (is.integer(selectMod)) selection3 <- selectMod
}
}
}
if (habillage == "quali") {
aux <- 1
col.var <- NULL
for (j in res.mca$call$quali) {
col.var <- c(col.var,rep(aux,nlevels(res.mca$call$X[,j])))
aux <- aux + 1
}
if (!is.null(res.mca$call$quali.sup)){
col.quali.sup <- NULL
for (j in res.mca$call$quali.sup) {
col.quali.sup <- c(col.quali.sup,rep(aux,nlevels(res.mca$call$X[,j])))
aux <- aux + 1
}
}
}
if (!(habillage %in% c("none","quali","cos2","contrib"))) {
if (!is.factor(res.mca$call$X[,habillage])) stop("The variable ", habillage, " is not qualitative")
col.ind <- as.numeric(as.factor(res.mca$call$X[, habillage]))
n.mod <- nlevels(as.factor(res.mca$call$X[, habillage]))
col.ind.sup <- col.ind[res.mca$call$ind.sup]
if (!is.null(res.mca$call$ind.sup)) col.ind <- col.ind[-res.mca$call$ind.sup]
}
# if (habillage == "none" & graph.type == "classic") {
if (habillage == "none") {
if (length(col.var)==1) col.var <- rep(col.var,nrow(coord.var))
if (!is.null(res.mca$call$quali.sup) & length(col.quali.sup)==1) col.quali.sup <- rep(col.quali.sup,nrow(coord.quali.sup))
}
titre <- title
if (is.null(title)) titre <- "MCA factor map"
if (is.na(test.invisible[1])|is.na(test.invisible[2])|is.na(test.invisible[4])|is.na(test.invisible[5])) {
if ((new.plot)&!nzchar(Sys.getenv("RSTUDIO_USER_IDENTITY"))) dev.new(width=min(14,max(8,8*diff(xlim)/diff(ylim))),height=8)
# if (is.null(palette)) palette = c("black","red","green3","blue","cyan","magenta","darkgray","darkgoldenrod","darkgreen","violet","turquoise","orange","lightpink","lavender","yellow","lightgreen","lightgrey","lightblue","darkkhaki", "darkmagenta","darkolivegreen","lightcyan", "darkorange", "darkorchid","darkred","darksalmon","darkseagreen","darkslateblue","darkslategray","darkslategrey","darkturquoise","darkviolet", "lightgray","lightsalmon","lightyellow", "maroon")
if (graph.type == "classic"){
plot(0, 0, main = titre, xlab = lab.x, ylab = lab.y, xlim = xlim, ylim = ylim, col = "white", asp=1, ...)
abline(v=0,lty=2, ...)
abline(h=0,lty=2, ...)
}
df_ind2a <- df_ind2b <- df_var <- df_quali.sup <- df_quanti.sup <- NULL
coo <- labe <- coll <- ipch <- fonte <- NULL
if (is.na(test.invisible[1])) {
coo <- rbind(coo,coord.ind)
if (lab.ind){ labe <- c(labe,rownames(coord.ind))
} else labe <- c(labe,rep("",nrow(coord.ind)))
if (length(col.ind)==1) coll <- c(coll,rep(col.ind,nrow(coord.ind)))
else coll <- c(coll,col.ind)
if (!is.null(select)) {
if (is.numeric(unselect)) coll[!((1:length(coll))%in%selection)] <- rgb(t(col2rgb(coll[!((1:length(coll))%in%selection)])),alpha=255*(1-unselect),maxColorValue=255)
else coll[!((1:length(coll))%in%selection)] <- unselect
labe[!((1:length(labe))%in%selection)] <- ""
}
ipch <- c(ipch,rep(16,nrow(coord.ind)))
fonte <- c(fonte,rep(1,nrow(coord.ind)))
if (graph.type == "ggplot") df_ind2a <- data.frame(labe,coord.ind,coll,ipch,fonte)
}
if (is.na(test.invisible[2])) {
coo <- rbind(coo,coord.var)
if (lab.var){ labe2 <- rownames(coord.var)
} else labe2 <- rep("",nrow(coord.var))
coll2 <- col.var
if(graph.type == "ggplot"){
if(length(col.var) == 1) coll2 <- rep(col.var, nrow(coord.var))
else{coll2 <- col.var[1:nrow(coord.var)]}
}
if (!is.null(selectMod)) {
if (is.numeric(unselect)) coll2[!((1:length(coll2))%in%selection2)] <- rgb(t(col2rgb(coll2[!((1:length(coll2))%in%selection2)])),alpha=255*(1-unselect),maxColorValue=255)
else coll2[!((1:length(coll2))%in%selection2)] <- unselect
labe2[!((1:length(labe2))%in%selection2)] <- ""
}
if (graph.type == "ggplot") df_var <- data.frame(labe2,coord.var,coll2,rep(17,nrow(coord.var)),rep(1,nrow(coord.var)))
coll <- c(coll,coll2)
labe <- c(labe,labe2)
ipch <- c(ipch,rep(17,nrow(coord.var)))
fonte <- c(fonte,rep(1,nrow(coord.var)))
}
if (!is.null(res.mca$quali.sup) & is.na(test.invisible[5])) {
coo <- rbind(coo,coord.quali.sup)
if (lab.quali.sup){ labe2 <- rownames(coord.quali.sup)
} else labe2 <- rep("",nrow(coord.quali.sup))
coll2 <- col.quali.sup
# if((graph.type == "ggplot") & !(habillage %in% c("quali"))) coll2 <- rep(col.quali.sup, nrow(coord.quali.sup))
if ((!is.null(selectMod))&!is.null(selection3)) {
if (is.numeric(unselect)) coll2[!((1:length(coll2))%in%selection3)] <- rgb(t(col2rgb(coll2[!((1:length(coll2))%in%selection3)])),alpha=255*(1-unselect),maxColorValue=255)
else coll2[!((1:length(coll2))%in%selection3)] <- unselect
labe2[!((1:length(labe2))%in%selection3)] <- ""
}
if (length(selectMod)==1) {
if (grepl("contrib",selectMod)){
if (is.numeric(unselect)) coll2[1:length(coll2)] <- rgb(t(col2rgb(coll2[1:length(coll2)])),alpha=255*(1-unselect),maxColorValue=255)
else coll2[1:length(coll2)] <- unselect
labe2[1:length(coll2)] <- ""
}}
if (graph.type == "ggplot") df_quali.sup <- data.frame(labe2,coord.quali.sup,coll2,rep(17,nrow(coord.quali.sup)),rep(1,nrow(coord.quali.sup)))
coll <- c(coll,coll2)
labe <- c(labe,labe2)
ipch <- c(ipch,rep(17,nrow(coord.quali.sup)))
fonte <- c(fonte,rep(1,nrow(coord.quali.sup)))
}
if (!is.null(res.mca$ind.sup) & is.na(test.invisible[4])) {
coo <- rbind(coo,coord.ind.sup)
if (lab.ind.sup){ labe2 <- rownames(coord.ind.sup)
} else labe2 <- rep("",nrow(coord.ind.sup))
if (length(col.ind)==1) coll2 <- rep(col.ind.sup,nrow(coord.ind.sup))
else coll2 <- col.ind.sup
if ((!is.null(select))&!is.null(selectionS)) {
if (is.numeric(unselect)) coll2[!((1:length(coll2))%in%selectionS)] <- rgb(t(col2rgb(coll2[!((1:length(coll2))%in%selectionS)])),alpha=255*(1-unselect),maxColorValue=255)
else coll2[!((1:length(coll2))%in%selectionS)] <- unselect
labe2[!((1:length(labe2))%in%selectionS)] <- ""
}
if (!is.null(select)){
if (grepl("contrib",select)){
if (is.numeric(unselect)) coll2[1:length(coll2)] <- rgb(t(col2rgb(coll2[1:length(coll2)])),alpha=255*(1-unselect),maxColorValue=255)
else coll2[1:length(coll2)] <- unselect
labe2[1:length(coll2)] <- ""
}}
coll <- c(coll,coll2)
labe <- c(labe,labe2)
ipch <- c(ipch,rep(16,nrow(coord.ind.sup)))
fonte <- c(fonte,rep(1,nrow(coord.ind.sup)))
if (graph.type == "ggplot"){
df_ind2b <- data.frame(labe2,coord.ind.sup,coll2,rep(16,nrow(coord.ind.sup)),rep(1,nrow(coord.ind.sup)))
names(df_ind2b) <- names(df_ind2a)
}
}
if (graph.type == "ggplot"){
if(!is.null(df_var)) names(df_var) <- names(df_ind2a)
if(!is.null(df_quali.sup)) names(df_quali.sup) <- names(df_ind2a)
if(!is.null(df_quanti.sup)) names(df_quanti.sup) <- names(df_ind2a)
df_ind2 <- rbind(df_ind2a,df_ind2b)
}
if(graph.type == "classic"){
if ((habillage != "none")&(habillage != "quali")&(is.na(test.invisible[1])|is.na(test.invisible[2]))) {
L <- list(x="topleft", legend = levels(res.mca$call$X[,habillage]), text.col = 1:n.mod, cex = par("cex") * 0.8)
L <- modifyList(L, legend)
do.call(graphics::legend, L)
}
}
}
if(graph.type == "classic"){
if (shadowtext) points(coo[, 1], y = coo[, 2], pch = ipch, col = coll, ...)
if (any(labe!="")){
if (autoLab=="auto") autoLab <- (length(which(labe!=""))<50)
if (autoLab ==TRUE) autoLab(coo[labe!="", 1], y = coo[labe!="", 2], labels = labe[labe!=""], col = coll[labe!=""], font=fonte[labe!=""],shadotext=shadowtext,...)
if (autoLab ==FALSE) text(coo[labe!="", 1], y = coo[labe!="", 2], labels = labe[labe!=""], col = coll[labe!=""], font=fonte[labe!=""],pos=3,...)
}
if (!shadowtext) points(coo[, 1], y = coo[, 2], pch = ipch, col = coll, ...)
}
if (graph.type == "ggplot"){
gg_graph <- ggplot() +
coord_fixed(ratio = 1) +
xlim(xlim) + ylim(ylim) +
geom_hline(yintercept = 0,lty=ggoptions_default$line.lty, lwd = ggoptions_default$line.lwd, color=ggoptions_default$line.color) +
geom_vline(xintercept = 0,lty=ggoptions_default$line.lty, lwd = ggoptions_default$line.lwd, color=ggoptions_default$line.color) +
theme_light() + theme + labs(title = titre, x = lab.x, y= lab.y)
if (autoLab=="auto") autoLab <- (length(which(labe!=""))<50)
if(class(habillage) %in% c("numeric","integer")) habillage <- colnames(res.mca$call$X)[habillage]
transparency_ind <- 1
if (!is.null(select)) transparency_ind <- ifelse(rownames(df_ind2) %in% labe, 1, 1-unselect)
if (!(habillage %in% c("contrib","cos2"))){
if(habillage %in% c("none","quali")){
if(!is.null(df_ind2)){
gg_graph <- gg_graph +
geom_point(aes(x=df_ind2[,2], y=df_ind2[,3]), color= df_ind2[,4], shape = df_ind2[,5], size = ggoptions_default$size/2.8)
if(autoLab) text <- ggrepel::geom_text_repel(aes(x=df_ind2[,2], y=df_ind2[,3], label=df_ind2[,1]), size = ggoptions_default$size, color = df_ind2[,4], fontface = df_ind2[,6])
else{text <- geom_text(aes(x=df_ind2[,2], y=df_ind2[,3], label=df_ind2[,1]), size = ggoptions_default$size, color = df_ind2[,4], hjust = (-sign(df_ind2[,2])+1)/2, vjust = -sign(df_ind2[,3])*0.75+0.25, fontface = df_ind2[,6])}
gg_graph <- gg_graph + text
}
if(!is.null(df_var)){
if(autoLab) text_var <- ggrepel::geom_text_repel(aes(x=df_var[,2], y=df_var[,3], label=df_var[,1]), size = ggoptions_default$size, color = df_var[,4], fontface = df_var[,6])
else{text_var <- geom_text(aes(x=df_var[,2], y=df_var[,3], label=df_var[,1]), size = ggoptions_default$size, color = df_var[,4], hjust = (-sign(df_var[,2])+1)/2, vjust = -sign(df_var[,3])*0.75+0.25, fontface = df_var[,6])}
gg_graph <- gg_graph + geom_point(aes(x=df_var[,2], y=df_var[,3]), color= df_var[,4], shape = df_var[,5], size = ggoptions_default$size/2.8) + text_var
}
if(!is.null(df_quali.sup)){
if(autoLab) text_quali.sup <- ggrepel::geom_text_repel(aes(x=df_quali.sup[,2], y=df_quali.sup[,3], label=df_quali.sup[,1]), size = ggoptions_default$size, color = df_quali.sup[,4], fontface = df_quali.sup[,6])
else{text_quali.sup <- geom_text(aes(x=df_quali.sup[,2], y=df_quali.sup[,3], label=df_quali.sup[,1]), size = ggoptions_default$size, color = df_quali.sup[,4], hjust = (-sign(df_quali.sup[,2])+1)/2, vjust = -sign(df_quali.sup[,3])*0.75+0.25, fontface = df_quali.sup[,6])}
gg_graph <- gg_graph + geom_point(aes(x=df_quali.sup[,2], y=df_quali.sup[,3]), color= df_quali.sup[,4], shape = df_quali.sup[,5], size = ggoptions_default$size/2.8) + text_quali.sup
}
} else{
if(is.na(test.invisible[1]) || is.na(test.invisible[4]) & !is.null(df_ind2)){
gg_graph <- gg_graph +
geom_point(aes(x=df_ind2[,2], y=df_ind2[,3], color= (res.mca$call$X)[rownames(df_ind2),habillage]), shape = df_ind2[,5], alpha = transparency_ind, size = ggoptions_default$size/2.8) +
scale_color_manual(values = palette[1:length(levels(res.mca$call$X[rownames(df_ind2),habillage]))], labels = levels(res.mca$call$X[,habillage])) +
labs(color = ifelse(legend["title"] %in% legend, legend["title"][[1]], habillage))
if(autoLab)text <- ggrepel::geom_text_repel(aes(x=df_ind2[,2], y=df_ind2[,3], label=df_ind2[,1]), size = ggoptions_default$size, color = df_ind2[,4], fontface = df_ind2[,6])
else{text <- geom_text(aes(x=df_ind2[,2], y=df_ind2[,3], label=df_ind2[,1]), size = ggoptions_default$size, color = df_ind2[,4], hjust = (-sign(df_ind2[,2])+1)/2, vjust = -sign(df_ind2[,3])*0.75+0.25, fontface = df_ind2[,6])}
gg_graph <- gg_graph + text
}
if(is.na(test.invisible[2]) & !is.null(df_var)){
if (habillage %in% res.mca$call$quali){
gg_graph <- gg_graph +
geom_point(aes(x=df_var[levels(res.mca$call$X[,habillage]),2], y=df_var[levels(res.mca$call$X[,habillage]),3]), color= palette[1:length(levels(res.mca$call$X[,habillage]))], shape = df_var[,5], size = ggoptions_default$size/2.8)
if(autoLab) text_var <- ggrepel::geom_text_repel(aes(x=df_var[levels(res.mca$call$X[,habillage]),2], y=df_var[levels(res.mca$call$X[,habillage]),3], label=levels(res.mca$call$X[,habillage])), size = ggoptions_default$size, color = palette[1:length(levels(res.mca$call$X[,habillage]))], fontface = df_var[levels(res.mca$call$X[,habillage]),6])
else{text_var <- geom_text(aes(x=df_var[levels(res.mca$call$X[,habillage]),2], y=df_var[levels(res.mca$call$X[,habillage]),3], label=levels(res.mca$call$X[,habillage])), size = ggoptions_default$size, color = palette[1:length(levels(res.mca$call$X[,habillage]))], fontface = df_var[levels(res.mca$call$X[,habillage]),6])}
gg_graph <- gg_graph + text_var
}
df_var.nohab <- df_var[which(!(rownames(res.mca$var$coord) %in% levels(res.mca$call$X[,habillage]))), ,drop = FALSE]
gg_graph <- gg_graph +
geom_point(aes(x = df_var.nohab[,2], y = df_var.nohab[,3]), size = ggoptions_default$size/2.8, color = df_var.nohab[,4], shape = 0)
if (autoLab) text_var <- ggrepel::geom_text_repel(aes(x = df_var.nohab[,2], y = df_var.nohab[,3], label = df_var.nohab[,1]), color = col.var[1], size = ggoptions_default$size, fontface = df_var.nohab[,6])
else{text_var <- geom_text(aes(x = df_var.nohab[,2], y = df_var.nohab[,3], label = df_var.nohab[,1]), color = col.var[1], size = ggoptions_default$size, fontface = df_var.nohab[,6],hjust = (-sign(df_var.nohab[,2])+1)/2, vjust = -sign(df_var.nohab[,3])*0.75+0.25)}
gg_graph <- gg_graph + text_var
}
if(is.na(test.invisible[5]) & !is.null(df_quali.sup)){
if (habillage %in% res.mca$call$quali.sup){
gg_graph <- gg_graph +
geom_point(aes(x = df_quali.sup[levels(res.mca$call$X[,habillage]),2], y = df_quali.sup[levels(res.mca$call$X[,habillage]),3]), size = ggoptions_default$size/2.8, color = palette[1:length(levels(res.mca$call$X[,habillage]))], shape = df_quali.sup[levels(res.mca$call$X[,habillage]),5])
if (autoLab) text_quali.sup.hab <- ggrepel::geom_text_repel(aes(x = df_quali.sup[levels(res.mca$call$X[,habillage]),2], y = df_quali.sup[levels(res.mca$call$X[,habillage]),3], label=levels(res.mca$call$X[,habillage])), color = palette[1:length(levels(res.mca$call$X[,habillage]))], size = ggoptions_default$size, fontface = df_quali.sup[levels(res.mca$call$X[,habillage]),6])
else{text_quali.sup.hab <- geom_text(aes(x = df_quali.sup[levels(res.mca$call$X[,habillage]),2], y = df_quali.sup[levels(res.mca$call$X[,habillage]),3], label=levels(res.mca$call$X[,habillage])), color = palette[1:length(levels(res.mca$call$X[,habillage]))], size = ggoptions_default$size, fontface = df_quali.sup[levels(res.mca$call$X[,habillage]),6],nudge_y=nudge_y)}
gg_graph <- gg_graph + text_quali.sup.hab
}
text_quali.sup <- NULL
if(nrow(res.mca$quali.sup$coord) > nlevels(res.mca$call$X[,habillage])){
df_quali.nohab <- df_quali.sup[which(!(rownames(res.mca$quali.sup$coord) %in% levels(res.mca$call$X[,habillage]))), ,drop = FALSE]
gg_graph <- gg_graph +
geom_point(aes(x = df_quali.nohab[,2], y = df_quali.nohab[,3]), size = ggoptions_default$size/2.8, color = col.quali.sup[1], shape = 0)
if (autoLab) text_quali.sup <- ggrepel::geom_text_repel(aes(x = df_quali.nohab[,2], y = df_quali.nohab[,3], label = df_quali.nohab[,1]), color = col.quali.sup[1], size = ggoptions_default$size, fontface = df_quali.nohab[,6])
else{text_quali.sup <- geom_text(aes(x = df_quali.nohab[,2], y = df_quali.nohab[,3], label = df_quali.nohab[,1]), color = col.quali.sup[1], size = ggoptions_default$size, fontface = df_quali.nohab[,6],hjust = (-sign(df_quali.nohab[,2])+1)/2, vjust = -sign(df_quali.nohab[,3])*0.75+0.25)}
gg_graph <- gg_graph + text_quali.sup
}
}
}
} else{
if(habillage == "cos2"){
coll_ind <- coll_var <- coll_quali.sup <- coll_ind.sup <- NULL
if(!is.null(res.mca$ind$cos2) & (is.na(test.invisible[1]))) coll_ind <- apply(res.mca$ind$cos2[,axes,drop = FALSE],1,FUN=sum)
if(!is.null(res.mca$var$cos2) & (is.na(test.invisible[2]))) coll_var <- apply(res.mca$var$cos2[,axes,drop = FALSE],1,FUN=sum)
if(!is.null(res.mca$quali.sup$cos2) & (is.na(test.invisible[5]))) coll_quali.sup <- apply(res.mca$quali.sup$cos2[,axes,drop = FALSE],1,FUN=sum)
if(!is.null(res.mca$ind.sup$cos2) & (is.na(test.invisible[4]))) coll_ind.sup <- apply(res.mca$ind.sup$cos2[,axes,drop = FALSE],1,FUN=sum)
}
if(habillage=="contrib"){
coll_ind <- coll_var <- coll_quali.sup <- coll_ind.sup <- NULL
if(!is.null(res.mca$ind$contrib) & (is.na(test.invisible[1]))) coll_ind <- res.mca$ind$contrib[,axes[1]]*res.mca$eig[axes[1],1] + res.mca$ind$contrib[,axes[2]]*res.mca$eig[axes[2],1]
if(!is.null(res.mca$var$contrib) & (is.na(test.invisible[2]))) coll_var <- res.mca$var$contrib[,axes[1]]*res.mca$eig[axes[1],1] + res.mca$var$contrib[,axes[2]]*res.mca$eig[axes[2],1]
if(!is.null(res.mca$quali.sup) & is.na(test.invisible[5])) coll_quali.sup <- rep(0, nrow(res.mca$quali.sup$coord))
if(!is.null(res.mca$ind.sup) & is.na(test.invisible[4])) coll_ind.sup <- rep(0, nrow(res.mca$ind.sup$coord))
}
df_ind2[,4] <- c(coll_ind,coll_ind.sup)
df_var[,4] <- coll_var
df_quali.sup[,4] <- coll_quali.sup
if(is.na(test.invisible[1])){
gg_graph <- gg_graph +
geom_point(aes(x=df_ind2[,2], y=df_ind2[,3], color = df_ind2[,4]), shape = df_ind2[,5], alpha = transparency_ind, size = ggoptions_default$size/2.8)
if (autoLab) text <- ggrepel::geom_text_repel(aes(x=df_ind2[,2], y=df_ind2[,3], label=df_ind2[,1], color = df_ind2[,4]), size = ggoptions_default$size, show.legend = FALSE,fontface=df_ind2[,6])
else{text <- geom_text(aes(x=df_ind2[,2], y=df_ind2[,3], label=df_ind2[,1], color = df_ind2[,4]), size = ggoptions_default$size, show.legend = FALSE, hjust = (-sign(df_ind2[,2])+1)/2, vjust = -sign(df_ind2[,3])*0.75+0.25,fontface=df_ind2[,6])}
gg_graph <- gg_graph + text
}
if(is.na(test.invisible[2]) & !is.null(df_var)){
gg_graph <- gg_graph + geom_point(aes(x=df_var[,2], y=df_var[,3], color= df_var[,4]), shape = df_var[,5], size = ggoptions_default$size/2.8)
if(autoLab) text_var <- ggrepel::geom_text_repel(aes(x=df_var[,2], y=df_var[,3], label=df_var[,1], color = df_var[,4]), size = ggoptions_default$size, fontface = df_var[,6])
else{text_var <- geom_text(aes(x=df_var[,2], y=df_var[,3], label=df_var[,1], color = df_var[,4]), size = ggoptions_default$size, fontface = df_var[,6])}
gg_graph <- gg_graph + text_var
}
if(is.na(test.invisible[5]) & !is.null(df_quali.sup)){
gg_graph <- gg_graph + geom_point(aes(x = df_quali.sup[,2], y = df_quali.sup[,3], color = df_quali.sup[,4]), size = ggoptions_default$size/2.8, shape = df_quali.sup[,5])
if (autoLab) text_quali.sup <- ggrepel::geom_text_repel(aes(x = df_quali.sup[,2], y = df_quali.sup[,3], label=df_quali.sup[,1], color = df_quali.sup[,4]), size = ggoptions_default$size, fontface = df_quali.sup[,6])
else{text_quali.sup <- geom_text(aes(x = df_quali.sup[,2], y = df_quali.sup[,3], label=df_quali.sup[,1], color = df_quali.sup[,4]), size = ggoptions_default$size, fontface = df_quali.sup[,6])}
gg_graph <- gg_graph + text_quali.sup
}
gg_graph <- gg_graph + scale_color_gradient(low=ggoptions_default$low.col.quanti, high=ggoptions_default$high.col.quanti) + labs(color = ifelse(legend["title"] %in% legend, legend["title"][[1]], habillage))
}
}
}
if (choix == "quanti.sup") {
gg_graph <- NULL
if (!is.null(res.mca$quanti.sup)) {
if ((new.plot)&!nzchar(Sys.getenv("RSTUDIO_USER_IDENTITY"))) dev.new()
# if (is.null(palette)) palette(c("black","red","green3","blue","cyan","magenta","darkgray","darkgoldenrod","darkgreen","violet","turquoise","orange","lightpink","lavender","yellow","lightgreen","lightgrey","lightblue","darkkhaki", "darkmagenta","darkolivegreen","lightcyan", "darkorange", "darkorchid","darkred","darksalmon","darkseagreen","darkslateblue","darkslategray","darkslategrey","darkturquoise","darkviolet", "lightgray","lightsalmon","lightyellow", "maroon"))
if (is.null(title)) title <- "Supplementary quantitative variables"
if(graph.type=="classic"){
plot(0, 0, main = title, xlab = lab.x, ylab = lab.y, xlim = c(-1.1,1.1), ylim = c(-1.1,1.1), col = "white", asp=1, ...)
abline(v=0,lty=2, ...)
abline(h=0,lty=2, ...)
x.cercle <- seq(-1, 1, by = 0.01)
y.cercle <- sqrt(1 - x.cercle^2)
lines(x.cercle, y = y.cercle,...)
lines(x.cercle, y = -y.cercle,...)
}
if (!is.null(select)) {
if (mode(select)=="numeric") selection <- select
else {
if (sum(rownames(res.mca$quanti.sup$coord)%in%select)!=0) selection <- which(rownames(res.mca$quanti.sup$coord)%in%select)
else {
if (grepl("coord",select)) selection <- (rev(order(apply(res.mca$quanti.sup$coord[,axes]^2,1,sum))))[1:min(nrow(res.mca$quanti.sup$coord),sum(as.integer(unlist(strsplit(select,"coord"))),na.rm=T))]
if (is.integer(select)) selection <- select
}
}
res.mca$quanti.sup$coord <- res.mca$quanti.sup$coord[selection,,drop=FALSE]
}
if(graph.type=="classic"){
for (v in 1:nrow(res.mca$quanti.sup$coord)) {
arrows(0, 0, res.mca$quanti.sup$coord[v, axes[1]], res.mca$quanti.sup$coord[v, axes[2]], length = 0.1, angle = 15, code = 2, col = col.quanti.sup,...)
if (abs(res.mca$quanti.sup$coord[v,axes[1]])>abs(res.mca$quanti.sup$coord[v,axes[2]])){
if (res.mca$quanti.sup$coord[v,axes[1]]>=0) pos<-4
else pos<-2
}
else {
if (res.mca$quanti.sup$coord[v,axes[2]]>=0) pos<-3
else pos<-1
}
if((!is.null(label)) && (label=="all" | "quanti.sup" %in% label)){
text(res.mca$quanti.sup$coord[v, axes[1]], y = res.mca$quanti.sup$coord[v, axes[2]], labels = rownames(res.mca$quanti.sup$coord)[v], pos = pos, col = col.quanti.sup,...)
}
}
}
if(graph.type=="ggplot"){
if (autoLab=="auto") autoLab <- (length(which(rownames(res.mca$quanti.sup$coord)!=""))<50)
df_quanti.sup <- data.frame(rownames(res.mca$quanti.sup$coord),res.mca$quanti.sup$coord[,axes[1]],res.mca$quanti.sup$coord[,axes[2]])
circle <- annotate("path",
x=0+1*cos(seq(0,2*pi,length.out=100)),
y=0+1*sin(seq(0,2*pi,length.out=100)),
lty = ggoptions_default$circle.lty,
lwd = ggoptions_default$circle.lwd,
color = ggoptions_default$circle.color)
gg_graph <- ggplot() +
coord_fixed(ratio = 1) +
geom_line(aes(x=x, y=y), data=data.frame(x=-1:1,y=0),lty=ggoptions_default$line.lty, lwd = ggoptions_default$line.lwd, color=ggoptions_default$line.color) +
geom_line(aes(x=x, y=y), data=data.frame(x=0,y=-1:1),lty=ggoptions_default$line.lty, lwd = ggoptions_default$line.lwd, color=ggoptions_default$line.color) +
theme_light()
if(habillage=="none"){
gg_graph <- gg_graph +
aes(x=df_quanti.sup[,2], y=df_quanti.sup[,3]) +
geom_segment(aes(x=0,y=0,xend=df_quanti.sup[,2], yend=df_quanti.sup[,3]),arrow=arrow(length=unit(0.2,"cm")), lty = ggoptions_default$segment.lty, lwd = ggoptions_default$segment.lwd, color = col.quanti.sup)
if(autoLab) text <- ggrepel::geom_text_repel(aes(x=df_quanti.sup[,2], y=df_quanti.sup[,3],label=df_quanti.sup[,1]), size = ggoptions_default$size, color = col.quanti.sup)
else{text <- geom_text(aes(x=df_quanti.sup[,2], y=df_quanti.sup[,3],label=df_quanti.sup[,1]), size = ggoptions_default$size, color = col.quanti.sup, hjust = (-sign(df_quanti.sup[,2])+1)/2, vjust = -sign(df_quanti.sup[,3])*0.75+0.25)}
}
gg_graph <- gg_graph + text + theme + circle
gg_graph <- gg_graph + xlab(lab.x) + ylab(lab.y) + ggtitle(title)
}
}
}
if (choix == "var") {
lab.var <- lab.quali.sup <- lab.quanti.sup <- FALSE
if(length(label)==1 && label=="all") lab.var <- lab.quali.sup <- lab.quanti.sup <- TRUE
if("var" %in% label) lab.var<-TRUE
if("quali.sup" %in% label) lab.quali.sup<-TRUE
if("quanti.sup" %in% label) lab.quanti.sup<-TRUE
test.invisible <- vector(length = 3)
if (!is.null(invisible)) {
test.invisible[1] <- match("var", invisible)
test.invisible[2] <- match("quali.sup", invisible)
test.invisible[3] <- match("quanti.sup", invisible)
}
else test.invisible <- rep(NA, 3)
if ((new.plot)&!nzchar(Sys.getenv("RSTUDIO_USER_IDENTITY"))) dev.new()
# if (is.null(palette)) palette(c("black","red","green3","blue","cyan","magenta","darkgray","darkgoldenrod","darkgreen","violet","turquoise","orange","lightpink","lavender","yellow","lightgreen","lightgrey","lightblue","darkkhaki", "darkmagenta","darkolivegreen","lightcyan", "darkorange", "darkorchid","darkred","darksalmon","darkseagreen","darkslateblue","darkslategray","darkslategrey","darkturquoise","darkviolet", "lightgray","lightsalmon","lightyellow", "maroon"))
if (is.null(xlim)) xlim <- c(0,1)
if (is.null(ylim)) ylim <- c(0,1)
if (graph.type == "classic"){
plot(0, 0, main = title, xlab = lab.x, ylab = lab.y, xlim = xlim, ylim = ylim, col = "white", asp=1, ...)
abline(v=0,lty=2, ...)
abline(h=0,lty=2, ...)
}
if (is.null(title)) title <- "Variables representation"
coo <- labe <- coll <- ipch <- fonte <- NULL
coord.actif <- res.mca$var$eta2[, axes,drop=FALSE]
if (!is.null(res.mca$quali.sup$eta2)) coord.illu <- res.mca$quali.sup$eta2[,axes,drop=FALSE]
if (!is.null(res.mca$quanti.sup$coord)) coord.illuq <- res.mca$quanti.sup$coord[,axes,drop=FALSE]^2
if (is.na(test.invisible[1])){
coo <- rbind(coo,coord.actif)
if (lab.var){ labe <- c(labe,rownames(coord.actif))
} else labe <- c(labe,rep("",nrow(coord.actif)))
if (length(col.var)==1) coll <- c(coll,rep(col.var,nrow(coord.actif)))
else coll <- col.var
ipch <- c(ipch,rep(20,nrow(coord.actif)))
fonte <- c(fonte,rep(1,nrow(coord.actif)))
}
if ((!is.null(res.mca$quali.sup$eta2))&&(is.na(test.invisible[2]))){
coo <- rbind(coo,coord.illu)
if (lab.quali.sup){ labe <- c(labe,rownames(coord.illu))
} else labe <- c(labe,rep("",nrow(coord.illu)))
if (length(col.quali.sup)==1) coll <- c(coll,rep(col.quali.sup,nrow(coord.illu)))
else coll <- c(coll,col.quali.sup)
ipch <- c(ipch,rep(1,nrow(coord.illu)))
fonte <- c(fonte,rep(3,nrow(coord.illu)))
}
if ((!is.null(res.mca$quanti.sup$coord))&&(is.na(test.invisible[3]))){
coo <- rbind(coo,coord.illuq)
if (lab.quanti.sup){ labe <- c(labe,rownames(coord.illuq))
} else labe <- c(labe,rep("",nrow(coord.illuq)))
if (length(col.quanti.sup)==1) coll <- c(coll,rep(col.quanti.sup,nrow(coord.illuq)))
else coll <- c(coll,col.quanti.sup)
ipch <- c(ipch,rep(1,nrow(coord.illuq)))
fonte <- c(fonte,rep(3,nrow(coord.illuq)))
}
### 22 mars 2018
selection <- NULL
if (!is.null(select)) {
if (mode(select)=="numeric") selection <- (rev(order(apply(coo^2,1,sum))))[1:min(nrow(coo), as.integer(select))]
else {
if (sum(rownames(coo)%in%select)!=0) selection <- which(rownames(coo)%in%select)
else {
if (grepl("coord",select)) selection <- (rev(order(apply(coo^2,1,sum))))[1:min(nrow(coo),sum(as.integer(unlist(strsplit(select,"coord"))),na.rm=T))]
if (is.integer(select)) selection <- select
}
}
}
if (!is.null(select)) {
if (is.numeric(unselect)) coll[!((1:length(coll))%in%selection)] <- rgb(t(col2rgb(coll[!((1:length(coll))%in%selection)])),alpha=255*(1-unselect),maxColorValue=255)
else coll[!((1:length(coll))%in%selection)] <- unselect
labe[!((1:length(labe))%in%selection)] <- ""
}
### Fin 22 mars 2018
if(graph.type== "classic"){
if (any(labe!="")){
if (autoLab=="auto") autoLab <- (length(which(labe!=""))<50)
if (autoLab ==TRUE) autoLab(coo[labe!="", 1], y = coo[labe!="", 2], labels = labe[labe!=""], col = coll[labe!=""], font=fonte[labe!=""],...)
if (autoLab ==FALSE) text(coo[labe!="", 1], y = coo[labe!="", 2], labels = labe[labe!=""], col = coll[labe!=""], font=fonte[labe!=""],pos=3,...)
}
points(coo[, 1], y = coo[, 2], pch = ipch, col = coll, ...)
}
if(graph.type == "ggplot"){
if (autoLab=="auto") autoLab <- (length(which(labe!=""))<50)
df_var <- data.frame(labe,coo,coll,ipch,fonte)
df_var[,5][which(df_var[,5] == 20)] <- 19
gg_graph <- ggplot() +
coord_fixed(ratio = 1) +
xlab(lab.x) + ylab(lab.y) +
xlim(xlim) + ylim(ylim) +
geom_hline(yintercept = 0,lty=ggoptions_default$line.lty, lwd = ggoptions_default$line.lwd, color=ggoptions_default$line.color) +
geom_vline(xintercept = 0,lty=ggoptions_default$line.lty, lwd = ggoptions_default$line.lwd, color=ggoptions_default$line.color) +
theme_light() +
ggoptions_default$theme +
ggtitle(title)
if(habillage == "none"){
gg_graph <- gg_graph + geom_point(aes(x=df_var[,2], y=df_var[,3]), color= df_var[,4], shape = df_var[,5])
if(autoLab) text <- ggrepel::geom_text_repel(aes(x=df_var[,2], y=df_var[,3], label=df_var[,1]), size = ggoptions_default$size, color = df_var[,4], fontface = df_var[,6])
else{text <- geom_text(aes(x=df_var[,2], y=df_var[,3], label=df_var[,1]), size = ggoptions_default$size, color = df_var[,4], hjust = (-sign(df_var[,2])+1)/2, vjust = -sign(df_var[,3])*0.75+0.25, fontface = df_var[,6])}
gg_graph <- gg_graph + text
}
# if(habillage == "cos2"){
# df_ind <- NULL
# if(is.na(test.invisible[1])) df_ind <- rbind(df_ind, df_var[rownames(res.mca$var$eta2), ,drop = FALSE])
# if(is.na(test.invisible[2])) df_ind <- rbind(df_ind, df_var[rownames(res.mca$quali.sup$eta2), ,drop = FALSE])
# #if(is.na(test.invisible[3])) df_ind <- rbind(df_ind, df_var[rownames(res.mca$quanti.sup$coord), ,drop = FALSE])
#
# coll_var <- coll_quali.sup <- coll_quanti.sup <- NULL
# if(!is.null(res.mca$var$cos2) & (is.na(test.invisible[1]))){
# coll_var <- apply(res.mca$var$cos2[,axes,drop = FALSE],1,FUN=sum)}
# if(!is.null(res.mca$quali.sup$cos2) & (is.na(test.invisible[2]))){
# coll_quali.sup <- apply(res.mca$quali.sup$cos2[,axes,drop = FALSE],1,FUN=sum)}
# # if(!is.null(res.mca$quanti.sup$cos2) & (is.na(test.invisible[3]))){
# # coll_quanti.sup <- apply(res.mca$quanti.sup$cos2[,axes,drop = FALSE],1,FUN=sum)}
# coll_quanti <- c(coll_var,coll_quali.sup,coll_quanti.sup)
# #df_ind[,4] <- coll_quanti
#
# gg_graph <- ggplot() +
# coord_fixed(ratio = 1) +
# geom_point(aes(x=df_ind[,2], y=df_ind[,3], color = df_ind[,4]), shape = df_ind[,5]) +
# xlab(lab.x) + ylab(lab.y) +
# xlim(xlim) + ylim(ylim) +
# geom_hline(yintercept = 0,lty=ggoptions_default$line.lty, lwd = ggoptions_default$line.lwd, color=ggoptions_default$line.color) +
# geom_vline(xintercept = 0,lty=ggoptions_default$line.lty, lwd = ggoptions_default$line.lwd, color=ggoptions_default$line.color) +
# scale_color_gradient(low=ggoptions_default$low.col.quanti, high=ggoptions_default$high.col.quanti) +
# labs(color = ifelse(legend["title"] %in% legend, legend["title"][[1]], "cos2")) +
# theme_light() +
# ggoptions_default$theme +
# ggtitle(title)
# if (autoLab) text <- ggrepel::geom_text_repel(aes(x=df_ind[,2], y=df_ind[,3], label=df_ind[,1], color = df_ind[,4]), size = ggoptions_default$size, show.legend = FALSE,fontface=df_ind[,6])
# else{text <- geom_text(aes(x=df_ind[,2], y=df_ind[,3], label=df_ind[,1], color = df_ind[,4]), size = ggoptions_default$size, show.legend = FALSE, nudge_y = nudge_y,fontface=df_ind[,6])}
# gg_graph <- gg_graph + text
# }
# if(habillage == "contrib"){
#
# }
gg_graph <- gg_graph + theme
}
}
palette(old.palette)
if(graph.type == "ggplot") return(gg_graph)
}
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plot.MCA <- function (x, axes = c(1, 2), choix=c("ind","var","quanti.sup"),
xlim = NULL, ylim = NULL, invisible = c("none","ind", "var", "ind.sup", "quali.sup", "quanti.sup"),
col.ind = "black", col.var = "red", col.quali.sup = "darkgreen",
col.ind.sup = "blue", col.quanti.sup = "blue",
label=c("all","none","ind", "var", "ind.sup", "quali.sup", "quanti.sup"), title = NULL, habillage = "none", palette=NULL,
autoLab = c("auto","yes","no"),new.plot=FALSE,select=NULL,selectMod=NULL, unselect=0.7, shadowtext=FALSE,
legend = list(bty = "y", x = "topleft"), graph.type = c("ggplot","classic"), ggoptions = NULL, ...){
label <- match.arg(label,c("all","none","ind", "var", "ind.sup", "quali.sup", "quanti.sup"),several.ok=TRUE)
choix <- match.arg(choix,c("ind","var","quanti.sup"))
graph.type <- match.arg(graph.type[1],c("ggplot","classic"))
autoLab <- match.arg(autoLab,c("auto","yes","no"))
argument <- list(...)
if (!is.null(argument[["cex"]]) & is.null(ggoptions["size"])) ggoptions["size"] <- 4*argument$cex
ggoptions_default <- list(size = 4, point.shape = 19, line.lty = 2, line.lwd = 0.5, line.color = "black", segment.lty = 1, segment.lwd = 0.5, circle.lty = 1, circle.lwd = 0.5, circle.color = "black", low.col.quanti = "blue", high.col.quanti = "red3")
if (!is.null(ggoptions[1])) ggoptions_default[names(ggoptions)] <- ggoptions[names(ggoptions)]
old.palette <- palette()
if (is.null(palette)) palette <- c("black", "red", "green3", "blue", "magenta", "darkgoldenrod","darkgray", "orange", "cyan", "violet", "lightpink", "lavender", "yellow", "darkgreen","turquoise", "lightgrey", "lightblue", "darkkhaki","darkmagenta","lightgreen", "darkolivegreen", "lightcyan", "darkorange","darkorchid", "darkred", "darksalmon", "darkseagreen","darkslateblue", "darkslategray", "darkslategrey","darkturquoise", "darkviolet", "lightgray", "lightsalmon","lightyellow", "maroon")
palette(palette) # that is necessary
if (autoLab=="yes") autoLab <- TRUE
if (autoLab=="no") autoLab <- FALSE
invisible <- match.arg(invisible,c("none","ind", "var", "ind.sup", "quali.sup", "quanti.sup"),several.ok=TRUE)
if ("none"%in%invisible) invisible <- NULL
res.mca <- x
if (!inherits(res.mca, "MCA")) stop("non convenient data")
if (is.numeric(unselect)) if ((unselect>1)|(unselect<0)) stop("unselect should be betwwen 0 and 1")
lab.x <- paste("Dim ",axes[1]," (",format(res.mca$eig[axes[1],2],nsmall=2,digits=2),"%)",sep="")
lab.y <- paste("Dim ",axes[2]," (",format(res.mca$eig[axes[2],2],nsmall=2,digits=2),"%)",sep="")
if (graph.type == "ggplot"){
theme <- theme(
axis.title = element_text(hjust = 1, size = if (is.null(argument[["cex.axis"]])) {10} else {10*argument$cex.axis},face = 2),
plot.title = element_text(hjust = 0.5, size = if (is.null(argument[["cex.main"]])) {11} else {11*argument$cex.main},face = 2),
legend.position = ifelse(legend$x %in% c("bottom","up","right","left"), legend$x, "right"),
legend.box.spacing=unit(0.1, 'cm'),legend.margin=margin()
)
}
if (choix =="ind"){
lab.ind <- lab.var <- lab.quali.sup <- lab.ind.sup <- FALSE
if(length(label)==1 && label=="all") lab.ind <- lab.var <- lab.quali.sup <- lab.ind.sup <- TRUE
if("ind" %in% label) lab.ind<-TRUE
if("var" %in% label) lab.var<-TRUE
if("quali.sup" %in% label) lab.quali.sup<-TRUE
if("ind.sup" %in% label) lab.ind.sup<-TRUE
test.invisible <- vector(length = 5)
if (!is.null(invisible)) {
test.invisible[1] <- match("ind", invisible)
test.invisible[2] <- match("var", invisible)
test.invisible[3] <- match("quanti.sup", invisible)
test.invisible[4] <- match("ind.sup", invisible)
test.invisible[5] <- match("quali.sup", invisible)
}
else test.invisible <- rep(NA, 5)
coord.var <- res.mca$var$coord[, axes]
coord.ind <- res.mca$ind$coord[, axes]
coord.ind.sup <- coord.quali.sup <- NULL
if (!is.null(res.mca$ind.sup)) coord.ind.sup <- res.mca$ind.sup$coord[, axes,drop=FALSE]
if (!is.null(res.mca$quali.sup)) coord.quali.sup <- res.mca$quali.sup$coord[, axes,drop=FALSE]
nullxlimylim <- (is.null(xlim) & is.null(ylim))
if (is.null(xlim)) {
xmin <- xmax <- 0
if(is.na(test.invisible[1])) xmin <- min(xmin, coord.ind[,1])
if(is.na(test.invisible[1])) xmax <- max(xmax, coord.ind[,1])
if(is.na(test.invisible[4])) xmin <- min(xmin, coord.ind.sup[, 1])
if(is.na(test.invisible[4])) xmax <- max(xmax, coord.ind.sup[, 1])
if(is.na(test.invisible[2])) xmin <- min(xmin, coord.var[,1])
if(is.na(test.invisible[2])) xmax <- max(xmax, coord.var[,1])
if(is.na(test.invisible[5])) xmin <- min(xmin, coord.quali.sup[, 1])
if(is.na(test.invisible[5])) xmax <- max(xmax, coord.quali.sup[, 1])
# xlim <- c(xmin, xmax) * 1.2
xlim <- c(xmin, xmax)
xlim <- (xlim-mean(xlim))*1.2 + mean(xlim)
}
if (is.null(ylim)) {
ymin <- ymax <- 0
if(is.na(test.invisible[1])) ymin <- min(ymin, coord.ind[,2])
if(is.na(test.invisible[1])) ymax <- max(ymax, coord.ind[,2])
if(is.na(test.invisible[4])) ymin <- min(ymin, coord.ind.sup[, 2])
if(is.na(test.invisible[4])) ymax <- max(ymax, coord.ind.sup[, 2])
if(is.na(test.invisible[2])) ymin <- min(ymin, coord.var[,2])
if(is.na(test.invisible[2])) ymax <- max(ymax, coord.var[,2])
if(is.na(test.invisible[5])) ymin <- min(ymin, coord.quali.sup[,2])
if(is.na(test.invisible[5])) ymax <- max(ymax, coord.quali.sup[,2])
# ylim <- c(ymin, ymax) * 1.2
ylim <- c(ymin, ymax)
ylim <- (ylim-mean(ylim))*1.2 + mean(ylim)
}
if (nullxlimylim & diff(xlim)/diff(ylim)>3) ylim <- (ylim-mean(ylim))*diff(xlim)/diff(ylim)/3 + mean(ylim)
if (nullxlimylim & diff(xlim)/diff(ylim)<1/2) xlim <- (xlim-mean(xlim))*diff(ylim)/diff(xlim)/2 + mean(xlim)
if(graph.type=="ggplot") nudge_y <- (ylim[2] - ylim[1])*0.03
selection <- selectionS <- selection2 <- selection3 <- NULL
if (!is.null(select)) {
if (mode(select)=="numeric") selection <- select
else {
if (sum(rownames(res.mca$ind$coord)%in%select)!=0) selection <- which(rownames(res.mca$ind$coord)%in%select)
else {
if (grepl("contrib",select)) selection <- (rev(order(res.mca$ind$contrib[,axes[1],drop=FALSE]*res.mca$eig[axes[1],1]+res.mca$ind$contrib[,axes[2],drop=FALSE]*res.mca$eig[axes[2],1])))[1:min(nrow(res.mca$ind$coord),sum(as.integer(unlist(strsplit(select,"contrib"))),na.rm=T))]
# if (grepl("contrib",select)) selection <- (rev(order(apply(res.mca$ind$contrib[,axes,drop=FALSE],1,sum))))[1:min(nrow(res.mca$ind$coord),sum(as.integer(unlist(strsplit(select,"contrib"))),na.rm=T))]
if (grepl("coord",select)) selection <- (rev(order(apply(res.mca$ind$coord[,axes,drop=FALSE]^2,1,sum))))[1:min(nrow(res.mca$ind$coord),sum(as.integer(unlist(strsplit(select,"coord"))),na.rm=T))]
if (grepl("cos2",select)) {
if (sum(as.numeric(unlist(strsplit(select,"cos2"))),na.rm=T)>=1) selection <- (rev(order(apply(res.mca$ind$cos2[,axes,drop=FALSE],1,sum))))[1:min(nrow(res.mca$ind$coord),sum(as.numeric(unlist(strsplit(select,"cos2"))),na.rm=T))]
else selection <- which(apply(res.mca$ind$cos2[,axes,drop=FALSE],1,sum)>sum(as.numeric(unlist(strsplit(select,"cos2"))),na.rm=T))
}
if (is.integer(select)) selection <- select
}
}
}
if (!is.null(select)&(!is.null(res.mca$call$ind.sup))) {
if (mode(select)=="numeric") selectionS <- select
else {
if (sum(rownames(res.mca$ind.sup$coord)%in%select)!=0) selectionS <- which(rownames(res.mca$ind.sup$coord)%in%select)
else {
if (grepl("contrib",select)) selectionS <- NULL
if (grepl("coord",select)) selectionS <- (rev(order(apply(res.mca$ind.sup$coord[,axes,drop=FALSE]^2,1,sum))))[1:min(nrow(res.mca$ind.sup$coord),sum(as.integer(unlist(strsplit(select,"coord"))),na.rm=T))]
if (grepl("cos2",select)) {
if (sum(as.numeric(unlist(strsplit(select,"cos2"))),na.rm=T)>=1) selectionS <- (rev(order(apply(res.mca$ind.sup$cos2[,axes,drop=FALSE],1,sum))))[1:min(nrow(res.mca$ind.sup$coord),sum(as.numeric(unlist(strsplit(select,"cos2"))),na.rm=T))]
else selectionS <- which(apply(res.mca$ind.sup$cos2[,axes,drop=FALSE],1,sum)>sum(as.numeric(unlist(strsplit(select,"cos2"))),na.rm=T))
}
if (is.integer(select)) selectionS <- select
}
}
}
if (!is.null(selectMod)) {
if (mode(selectMod)=="numeric") selection2 <- selectMod
else {
if (sum(rownames(res.mca$var$coord)%in%selectMod)+sum(rownames(res.mca$quali.sup$coord)%in%selectMod)!=0) selection2 <- which(rownames(res.mca$var$coord)%in%selectMod)
else {
if (grepl("contrib",selectMod)) selection2 <- (rev(order(res.mca$var$contrib[,axes[1],drop=FALSE]*res.mca$eig[axes[1],1]+res.mca$var$contrib[,axes[2],drop=FALSE]*res.mca$eig[axes[2],1])))[1:min(nrow(res.mca$var$coord),sum(as.integer(unlist(strsplit(selectMod,"contrib"))),na.rm=T))]
if (grepl("coord",selectMod)) selection2 <- (rev(order(apply(res.mca$var$coord[,axes,drop=FALSE]^2,1,sum))))[1:min(nrow(res.mca$var$coord),sum(as.integer(unlist(strsplit(selectMod,"coord"))),na.rm=T))]
if (grepl("cos2",selectMod)) {
if (sum(as.numeric(unlist(strsplit(selectMod,"cos2"))),na.rm=T)>=1) selection2 <- (rev(order(apply(res.mca$var$cos2[,axes],1,sum))))[1:min(nrow(res.mca$var$coord),sum(as.numeric(unlist(strsplit(selectMod,"cos2"))),na.rm=T))]
else selection2 <- which(apply(res.mca$var$cos2[,axes],1,sum)>sum(as.numeric(unlist(strsplit(selectMod,"cos2"))),na.rm=T))
}
if (grepl("v.test",selectMod)) selection2 <- union(which(abs(res.mca$var$v.test[,axes[1],drop=FALSE])>sum(as.integer(unlist(strsplit(selectMod,"v.test"))),na.rm=T)),which(abs(res.mca$var$v.test[,axes[2],drop=FALSE])>sum(as.integer(unlist(strsplit(selectMod,"v.test"))),na.rm=T)))
if (is.integer(selectMod)) selection2 <- selectMod
}
}
}
if ((!is.null(selectMod))&(!is.null(res.mca$call$quali.sup))) {
if (mode(selectMod)=="numeric") selection3 <- selectMod
else {
if (sum(rownames(res.mca$var$coord)%in%selectMod)+sum(rownames(res.mca$quali.sup$coord)%in%selectMod)!=0) selection3 <- which(rownames(res.mca$quali.sup$coord)%in%selectMod)
else {
if (grepl("contrib",selectMod)) selection3 <- NULL
if (grepl("coord",selectMod)) selection3 <- (rev(order(apply(res.mca$quali.sup$coord[,axes,drop=FALSE]^2,1,sum))))[1:min(nrow(res.mca$quali.sup$coord),sum(as.integer(unlist(strsplit(selectMod,"coord"))),na.rm=T))]
if (grepl("cos2",selectMod)) {
if (sum(as.numeric(unlist(strsplit(selectMod,"cos2"))),na.rm=T)>=1) selection3 <- (rev(order(apply(res.mca$quali.sup$cos2[,axes,drop=FALSE],1,sum))))[1:min(nrow(res.mca$quali.sup$coord),sum(as.numeric(unlist(strsplit(selectMod,"cos2"))),na.rm=T))]
else selection3 <- which(apply(res.mca$quali.sup$cos2[,axes,drop=FALSE],1,sum)>sum(as.numeric(unlist(strsplit(selectMod,"cos2"))),na.rm=T))
}
if (grepl("v.test",selectMod)) selection3 <- union(which(abs(res.mca$quali.sup$v.test[,axes[1],drop=FALSE])>sum(as.integer(unlist(strsplit(selectMod,"v.test"))),na.rm=T)),which(abs(res.mca$quali.sup$v.test[,axes[2],drop=FALSE])>sum(as.integer(unlist(strsplit(selectMod,"v.test"))),na.rm=T)))
if (is.integer(selectMod)) selection3 <- selectMod
}
}
}
if (habillage == "quali") {
aux <- 1
col.var <- NULL
for (j in res.mca$call$quali) {
col.var <- c(col.var,rep(aux,nlevels(res.mca$call$X[,j])))
aux <- aux + 1
}
if (!is.null(res.mca$call$quali.sup)){
col.quali.sup <- NULL
for (j in res.mca$call$quali.sup) {
col.quali.sup <- c(col.quali.sup,rep(aux,nlevels(res.mca$call$X[,j])))
aux <- aux + 1
}
}
}
if (!(habillage %in% c("none","quali","cos2","contrib"))) {
if (!is.factor(res.mca$call$X[,habillage])) stop("The variable ", habillage, " is not qualitative")
col.ind <- as.numeric(as.factor(res.mca$call$X[, habillage]))
n.mod <- nlevels(as.factor(res.mca$call$X[, habillage]))
col.ind.sup <- col.ind[res.mca$call$ind.sup]
if (!is.null(res.mca$call$ind.sup)) col.ind <- col.ind[-res.mca$call$ind.sup]
}
# if (habillage == "none" & graph.type == "classic") {
if (habillage == "none") {
if (length(col.var)==1) col.var <- rep(col.var,nrow(coord.var))
if (!is.null(res.mca$call$quali.sup) & length(col.quali.sup)==1) col.quali.sup <- rep(col.quali.sup,nrow(coord.quali.sup))
}
titre <- title
if (is.null(title)) titre <- "MCA factor map"
if (is.na(test.invisible[1])|is.na(test.invisible[2])|is.na(test.invisible[4])|is.na(test.invisible[5])) {
if ((new.plot)&!nzchar(Sys.getenv("RSTUDIO_USER_IDENTITY"))) dev.new(width=min(14,max(8,8*diff(xlim)/diff(ylim))),height=8)
# if (is.null(palette)) palette = c("black","red","green3","blue","cyan","magenta","darkgray","darkgoldenrod","darkgreen","violet","turquoise","orange","lightpink","lavender","yellow","lightgreen","lightgrey","lightblue","darkkhaki", "darkmagenta","darkolivegreen","lightcyan", "darkorange", "darkorchid","darkred","darksalmon","darkseagreen","darkslateblue","darkslategray","darkslategrey","darkturquoise","darkviolet", "lightgray","lightsalmon","lightyellow", "maroon")
if (graph.type == "classic"){
plot(0, 0, main = titre, xlab = lab.x, ylab = lab.y, xlim = xlim, ylim = ylim, col = "white", asp=1, ...)
abline(v=0,lty=2, ...)
abline(h=0,lty=2, ...)
}
df_ind2a <- df_ind2b <- df_var <- df_quali.sup <- df_quanti.sup <- NULL
coo <- labe <- coll <- ipch <- fonte <- NULL
if (is.na(test.invisible[1])) {
coo <- rbind(coo,coord.ind)
if (lab.ind){ labe <- c(labe,rownames(coord.ind))
} else labe <- c(labe,rep("",nrow(coord.ind)))
if (length(col.ind)==1) coll <- c(coll,rep(col.ind,nrow(coord.ind)))
else coll <- c(coll,col.ind)
if (!is.null(select)) {
if (is.numeric(unselect)) coll[!((1:length(coll))%in%selection)] <- rgb(t(col2rgb(coll[!((1:length(coll))%in%selection)])),alpha=255*(1-unselect),maxColorValue=255)
else coll[!((1:length(coll))%in%selection)] <- unselect
labe[!((1:length(labe))%in%selection)] <- ""
}
ipch <- c(ipch,rep(16,nrow(coord.ind)))
fonte <- c(fonte,rep(1,nrow(coord.ind)))
if (graph.type == "ggplot") df_ind2a <- data.frame(labe,coord.ind,coll,ipch,fonte)
}
if (is.na(test.invisible[2])) {
coo <- rbind(coo,coord.var)
if (lab.var){ labe2 <- rownames(coord.var)
} else labe2 <- rep("",nrow(coord.var))
coll2 <- col.var
if(graph.type == "ggplot"){
if(length(col.var) == 1) coll2 <- rep(col.var, nrow(coord.var))
else{coll2 <- col.var[1:nrow(coord.var)]}
}
if (!is.null(selectMod)) {
if (is.numeric(unselect)) coll2[!((1:length(coll2))%in%selection2)] <- rgb(t(col2rgb(coll2[!((1:length(coll2))%in%selection2)])),alpha=255*(1-unselect),maxColorValue=255)
else coll2[!((1:length(coll2))%in%selection2)] <- unselect
labe2[!((1:length(labe2))%in%selection2)] <- ""
}
if (graph.type == "ggplot") df_var <- data.frame(labe2,coord.var,coll2,rep(17,nrow(coord.var)),rep(1,nrow(coord.var)))
coll <- c(coll,coll2)
labe <- c(labe,labe2)
ipch <- c(ipch,rep(17,nrow(coord.var)))
fonte <- c(fonte,rep(1,nrow(coord.var)))
}
if (!is.null(res.mca$quali.sup) & is.na(test.invisible[5])) {
coo <- rbind(coo,coord.quali.sup)
if (lab.quali.sup){ labe2 <- rownames(coord.quali.sup)
} else labe2 <- rep("",nrow(coord.quali.sup))
coll2 <- col.quali.sup
# if((graph.type == "ggplot") & !(habillage %in% c("quali"))) coll2 <- rep(col.quali.sup, nrow(coord.quali.sup))
if ((!is.null(selectMod))&!is.null(selection3)) {
if (is.numeric(unselect)) coll2[!((1:length(coll2))%in%selection3)] <- rgb(t(col2rgb(coll2[!((1:length(coll2))%in%selection3)])),alpha=255*(1-unselect),maxColorValue=255)
else coll2[!((1:length(coll2))%in%selection3)] <- unselect
labe2[!((1:length(labe2))%in%selection3)] <- ""
}
if (length(selectMod)==1) {
if (grepl("contrib",selectMod)){
if (is.numeric(unselect)) coll2[1:length(coll2)] <- rgb(t(col2rgb(coll2[1:length(coll2)])),alpha=255*(1-unselect),maxColorValue=255)
else coll2[1:length(coll2)] <- unselect
labe2[1:length(coll2)] <- ""
}}
if (graph.type == "ggplot") df_quali.sup <- data.frame(labe2,coord.quali.sup,coll2,rep(17,nrow(coord.quali.sup)),rep(1,nrow(coord.quali.sup)))
coll <- c(coll,coll2)
labe <- c(labe,labe2)
ipch <- c(ipch,rep(17,nrow(coord.quali.sup)))
fonte <- c(fonte,rep(1,nrow(coord.quali.sup)))
}
if (!is.null(res.mca$ind.sup) & is.na(test.invisible[4])) {
coo <- rbind(coo,coord.ind.sup)
if (lab.ind.sup){ labe2 <- rownames(coord.ind.sup)
} else labe2 <- rep("",nrow(coord.ind.sup))
if (length(col.ind)==1) coll2 <- rep(col.ind.sup,nrow(coord.ind.sup))
else coll2 <- col.ind.sup
if ((!is.null(select))&!is.null(selectionS)) {
if (is.numeric(unselect)) coll2[!((1:length(coll2))%in%selectionS)] <- rgb(t(col2rgb(coll2[!((1:length(coll2))%in%selectionS)])),alpha=255*(1-unselect),maxColorValue=255)
else coll2[!((1:length(coll2))%in%selectionS)] <- unselect
labe2[!((1:length(labe2))%in%selectionS)] <- ""
}
if (!is.null(select)){
if (grepl("contrib",select)){
if (is.numeric(unselect)) coll2[1:length(coll2)] <- rgb(t(col2rgb(coll2[1:length(coll2)])),alpha=255*(1-unselect),maxColorValue=255)
else coll2[1:length(coll2)] <- unselect
labe2[1:length(coll2)] <- ""
}}
coll <- c(coll,coll2)
labe <- c(labe,labe2)
ipch <- c(ipch,rep(16,nrow(coord.ind.sup)))
fonte <- c(fonte,rep(1,nrow(coord.ind.sup)))
if (graph.type == "ggplot"){
df_ind2b <- data.frame(labe2,coord.ind.sup,coll2,rep(16,nrow(coord.ind.sup)),rep(1,nrow(coord.ind.sup)))
names(df_ind2b) <- names(df_ind2a)
}
}
if (graph.type == "ggplot"){
if(!is.null(df_var)) names(df_var) <- names(df_ind2a)
if(!is.null(df_quali.sup)) names(df_quali.sup) <- names(df_ind2a)
if(!is.null(df_quanti.sup)) names(df_quanti.sup) <- names(df_ind2a)
df_ind2 <- rbind(df_ind2a,df_ind2b)
}
if(graph.type == "classic"){
if ((habillage != "none")&(habillage != "quali")&(is.na(test.invisible[1])|is.na(test.invisible[2]))) {
L <- list(x="topleft", legend = levels(res.mca$call$X[,habillage]), text.col = 1:n.mod, cex = par("cex") * 0.8)
L <- modifyList(L, legend)
do.call(graphics::legend, L)
}
}
}
if(graph.type == "classic"){
if (shadowtext) points(coo[, 1], y = coo[, 2], pch = ipch, col = coll, ...)
if (any(labe!="")){
if (autoLab=="auto") autoLab <- (length(which(labe!=""))<50)
if (autoLab ==TRUE) autoLab(coo[labe!="", 1], y = coo[labe!="", 2], labels = labe[labe!=""], col = coll[labe!=""], font=fonte[labe!=""],shadotext=shadowtext,...)
if (autoLab ==FALSE) text(coo[labe!="", 1], y = coo[labe!="", 2], labels = labe[labe!=""], col = coll[labe!=""], font=fonte[labe!=""],pos=3,...)
}
if (!shadowtext) points(coo[, 1], y = coo[, 2], pch = ipch, col = coll, ...)
}
if (graph.type == "ggplot"){
gg_graph <- ggplot() +
coord_fixed(ratio = 1) +
xlim(xlim) + ylim(ylim) +
geom_hline(yintercept = 0,lty=ggoptions_default$line.lty, lwd = ggoptions_default$line.lwd, color=ggoptions_default$line.color) +
geom_vline(xintercept = 0,lty=ggoptions_default$line.lty, lwd = ggoptions_default$line.lwd, color=ggoptions_default$line.color) +
theme_light() + theme + labs(title = titre, x = lab.x, y= lab.y)
if (autoLab=="auto") autoLab <- (length(which(labe!=""))<50)
if(class(habillage) %in% c("numeric","integer")) habillage <- colnames(res.mca$call$X)[habillage]
transparency_ind <- 1
if (!is.null(select)) transparency_ind <- ifelse(rownames(df_ind2) %in% labe, 1, 1-unselect)
if (!(habillage %in% c("contrib","cos2"))){
if(habillage %in% c("none","quali")){
if(!is.null(df_ind2)){
gg_graph <- gg_graph +
geom_point(aes(x=df_ind2[,2], y=df_ind2[,3]), color= df_ind2[,4], shape = df_ind2[,5], size = ggoptions_default$size/2.8)
if(autoLab) text <- ggrepel::geom_text_repel(aes(x=df_ind2[,2], y=df_ind2[,3], label=df_ind2[,1]), size = ggoptions_default$size, color = df_ind2[,4], fontface = df_ind2[,6])
else{text <- geom_text(aes(x=df_ind2[,2], y=df_ind2[,3], label=df_ind2[,1]), size = ggoptions_default$size, color = df_ind2[,4], hjust = (-sign(df_ind2[,2])+1)/2, vjust = -sign(df_ind2[,3])*0.75+0.25, fontface = df_ind2[,6])}
gg_graph <- gg_graph + text
}
if(!is.null(df_var)){
if(autoLab) text_var <- ggrepel::geom_text_repel(aes(x=df_var[,2], y=df_var[,3], label=df_var[,1]), size = ggoptions_default$size, color = df_var[,4], fontface = df_var[,6])
else{text_var <- geom_text(aes(x=df_var[,2], y=df_var[,3], label=df_var[,1]), size = ggoptions_default$size, color = df_var[,4], hjust = (-sign(df_var[,2])+1)/2, vjust = -sign(df_var[,3])*0.75+0.25, fontface = df_var[,6])}
gg_graph <- gg_graph + geom_point(aes(x=df_var[,2], y=df_var[,3]), color= df_var[,4], shape = df_var[,5], size = ggoptions_default$size/2.8) + text_var
}
if(!is.null(df_quali.sup)){
if(autoLab) text_quali.sup <- ggrepel::geom_text_repel(aes(x=df_quali.sup[,2], y=df_quali.sup[,3], label=df_quali.sup[,1]), size = ggoptions_default$size, color = df_quali.sup[,4], fontface = df_quali.sup[,6])
else{text_quali.sup <- geom_text(aes(x=df_quali.sup[,2], y=df_quali.sup[,3], label=df_quali.sup[,1]), size = ggoptions_default$size, color = df_quali.sup[,4], hjust = (-sign(df_quali.sup[,2])+1)/2, vjust = -sign(df_quali.sup[,3])*0.75+0.25, fontface = df_quali.sup[,6])}
gg_graph <- gg_graph + geom_point(aes(x=df_quali.sup[,2], y=df_quali.sup[,3]), color= df_quali.sup[,4], shape = df_quali.sup[,5], size = ggoptions_default$size/2.8) + text_quali.sup
}
} else{
if(is.na(test.invisible[1]) || is.na(test.invisible[4]) & !is.null(df_ind2)){
gg_graph <- gg_graph +
geom_point(aes(x=df_ind2[,2], y=df_ind2[,3], color= (res.mca$call$X)[rownames(df_ind2),habillage]), shape = df_ind2[,5], alpha = transparency_ind, size = ggoptions_default$size/2.8) +
scale_color_manual(values = palette[1:length(levels(res.mca$call$X[rownames(df_ind2),habillage]))], labels = levels(res.mca$call$X[,habillage])) +
labs(color = ifelse(legend["title"] %in% legend, legend["title"][[1]], habillage))
if(autoLab)text <- ggrepel::geom_text_repel(aes(x=df_ind2[,2], y=df_ind2[,3], label=df_ind2[,1]), size = ggoptions_default$size, color = df_ind2[,4], fontface = df_ind2[,6])
else{text <- geom_text(aes(x=df_ind2[,2], y=df_ind2[,3], label=df_ind2[,1]), size = ggoptions_default$size, color = df_ind2[,4], hjust = (-sign(df_ind2[,2])+1)/2, vjust = -sign(df_ind2[,3])*0.75+0.25, fontface = df_ind2[,6])}
gg_graph <- gg_graph + text
}
if(is.na(test.invisible[2]) & !is.null(df_var)){
if (habillage %in% res.mca$call$quali){
gg_graph <- gg_graph +
geom_point(aes(x=df_var[levels(res.mca$call$X[,habillage]),2], y=df_var[levels(res.mca$call$X[,habillage]),3]), color= palette[1:length(levels(res.mca$call$X[,habillage]))], shape = df_var[,5], size = ggoptions_default$size/2.8)
if(autoLab) text_var <- ggrepel::geom_text_repel(aes(x=df_var[levels(res.mca$call$X[,habillage]),2], y=df_var[levels(res.mca$call$X[,habillage]),3], label=levels(res.mca$call$X[,habillage])), size = ggoptions_default$size, color = palette[1:length(levels(res.mca$call$X[,habillage]))], fontface = df_var[levels(res.mca$call$X[,habillage]),6])
else{text_var <- geom_text(aes(x=df_var[levels(res.mca$call$X[,habillage]),2], y=df_var[levels(res.mca$call$X[,habillage]),3], label=levels(res.mca$call$X[,habillage])), size = ggoptions_default$size, color = palette[1:length(levels(res.mca$call$X[,habillage]))], fontface = df_var[levels(res.mca$call$X[,habillage]),6])}
gg_graph <- gg_graph + text_var
}
df_var.nohab <- df_var[which(!(rownames(res.mca$var$coord) %in% levels(res.mca$call$X[,habillage]))), ,drop = FALSE]
gg_graph <- gg_graph +
geom_point(aes(x = df_var.nohab[,2], y = df_var.nohab[,3]), size = ggoptions_default$size/2.8, color = df_var.nohab[,4], shape = 0)
if (autoLab) text_var <- ggrepel::geom_text_repel(aes(x = df_var.nohab[,2], y = df_var.nohab[,3], label = df_var.nohab[,1]), color = col.var[1], size = ggoptions_default$size, fontface = df_var.nohab[,6])
else{text_var <- geom_text(aes(x = df_var.nohab[,2], y = df_var.nohab[,3], label = df_var.nohab[,1]), color = col.var[1], size = ggoptions_default$size, fontface = df_var.nohab[,6],hjust = (-sign(df_var.nohab[,2])+1)/2, vjust = -sign(df_var.nohab[,3])*0.75+0.25)}
gg_graph <- gg_graph + text_var
}
if(is.na(test.invisible[5]) & !is.null(df_quali.sup)){
if (habillage %in% res.mca$call$quali.sup){
gg_graph <- gg_graph +
geom_point(aes(x = df_quali.sup[levels(res.mca$call$X[,habillage]),2], y = df_quali.sup[levels(res.mca$call$X[,habillage]),3]), size = ggoptions_default$size/2.8, color = palette[1:length(levels(res.mca$call$X[,habillage]))], shape = df_quali.sup[levels(res.mca$call$X[,habillage]),5])
if (autoLab) text_quali.sup.hab <- ggrepel::geom_text_repel(aes(x = df_quali.sup[levels(res.mca$call$X[,habillage]),2], y = df_quali.sup[levels(res.mca$call$X[,habillage]),3], label=levels(res.mca$call$X[,habillage])), color = palette[1:length(levels(res.mca$call$X[,habillage]))], size = ggoptions_default$size, fontface = df_quali.sup[levels(res.mca$call$X[,habillage]),6])
else{text_quali.sup.hab <- geom_text(aes(x = df_quali.sup[levels(res.mca$call$X[,habillage]),2], y = df_quali.sup[levels(res.mca$call$X[,habillage]),3], label=levels(res.mca$call$X[,habillage])), color = palette[1:length(levels(res.mca$call$X[,habillage]))], size = ggoptions_default$size, fontface = df_quali.sup[levels(res.mca$call$X[,habillage]),6],nudge_y=nudge_y)}
gg_graph <- gg_graph + text_quali.sup.hab
}
text_quali.sup <- NULL
if(nrow(res.mca$quali.sup$coord) > nlevels(res.mca$call$X[,habillage])){
df_quali.nohab <- df_quali.sup[which(!(rownames(res.mca$quali.sup$coord) %in% levels(res.mca$call$X[,habillage]))), ,drop = FALSE]
gg_graph <- gg_graph +
geom_point(aes(x = df_quali.nohab[,2], y = df_quali.nohab[,3]), size = ggoptions_default$size/2.8, color = col.quali.sup[1], shape = 0)
if (autoLab) text_quali.sup <- ggrepel::geom_text_repel(aes(x = df_quali.nohab[,2], y = df_quali.nohab[,3], label = df_quali.nohab[,1]), color = col.quali.sup[1], size = ggoptions_default$size, fontface = df_quali.nohab[,6])
else{text_quali.sup <- geom_text(aes(x = df_quali.nohab[,2], y = df_quali.nohab[,3], label = df_quali.nohab[,1]), color = col.quali.sup[1], size = ggoptions_default$size, fontface = df_quali.nohab[,6],hjust = (-sign(df_quali.nohab[,2])+1)/2, vjust = -sign(df_quali.nohab[,3])*0.75+0.25)}
gg_graph <- gg_graph + text_quali.sup
}
}
}
} else{
if(habillage == "cos2"){
coll_ind <- coll_var <- coll_quali.sup <- coll_ind.sup <- NULL
if(!is.null(res.mca$ind$cos2) & (is.na(test.invisible[1]))) coll_ind <- apply(res.mca$ind$cos2[,axes,drop = FALSE],1,FUN=sum)
if(!is.null(res.mca$var$cos2) & (is.na(test.invisible[2]))) coll_var <- apply(res.mca$var$cos2[,axes,drop = FALSE],1,FUN=sum)
if(!is.null(res.mca$quali.sup$cos2) & (is.na(test.invisible[5]))) coll_quali.sup <- apply(res.mca$quali.sup$cos2[,axes,drop = FALSE],1,FUN=sum)
if(!is.null(res.mca$ind.sup$cos2) & (is.na(test.invisible[4]))) coll_ind.sup <- apply(res.mca$ind.sup$cos2[,axes,drop = FALSE],1,FUN=sum)
}
if(habillage=="contrib"){
coll_ind <- coll_var <- coll_quali.sup <- coll_ind.sup <- NULL
if(!is.null(res.mca$ind$contrib) & (is.na(test.invisible[1]))) coll_ind <- res.mca$ind$contrib[,axes[1]]*res.mca$eig[axes[1],1] + res.mca$ind$contrib[,axes[2]]*res.mca$eig[axes[2],1]
if(!is.null(res.mca$var$contrib) & (is.na(test.invisible[2]))) coll_var <- res.mca$var$contrib[,axes[1]]*res.mca$eig[axes[1],1] + res.mca$var$contrib[,axes[2]]*res.mca$eig[axes[2],1]
if(!is.null(res.mca$quali.sup) & is.na(test.invisible[5])) coll_quali.sup <- rep(0, nrow(res.mca$quali.sup$coord))
if(!is.null(res.mca$ind.sup) & is.na(test.invisible[4])) coll_ind.sup <- rep(0, nrow(res.mca$ind.sup$coord))
}
df_ind2[,4] <- c(coll_ind,coll_ind.sup)
df_var[,4] <- coll_var
df_quali.sup[,4] <- coll_quali.sup
if(is.na(test.invisible[1])){
gg_graph <- gg_graph +
geom_point(aes(x=df_ind2[,2], y=df_ind2[,3], color = df_ind2[,4]), shape = df_ind2[,5], alpha = transparency_ind, size = ggoptions_default$size/2.8)
if (autoLab) text <- ggrepel::geom_text_repel(aes(x=df_ind2[,2], y=df_ind2[,3], label=df_ind2[,1], color = df_ind2[,4]), size = ggoptions_default$size, show.legend = FALSE,fontface=df_ind2[,6])
else{text <- geom_text(aes(x=df_ind2[,2], y=df_ind2[,3], label=df_ind2[,1], color = df_ind2[,4]), size = ggoptions_default$size, show.legend = FALSE, hjust = (-sign(df_ind2[,2])+1)/2, vjust = -sign(df_ind2[,3])*0.75+0.25,fontface=df_ind2[,6])}
gg_graph <- gg_graph + text
}
if(is.na(test.invisible[2]) & !is.null(df_var)){
gg_graph <- gg_graph + geom_point(aes(x=df_var[,2], y=df_var[,3], color= df_var[,4]), shape = df_var[,5], size = ggoptions_default$size/2.8)
if(autoLab) text_var <- ggrepel::geom_text_repel(aes(x=df_var[,2], y=df_var[,3], label=df_var[,1], color = df_var[,4]), size = ggoptions_default$size, fontface = df_var[,6])
else{text_var <- geom_text(aes(x=df_var[,2], y=df_var[,3], label=df_var[,1], color = df_var[,4]), size = ggoptions_default$size, fontface = df_var[,6])}
gg_graph <- gg_graph + text_var
}
if(is.na(test.invisible[5]) & !is.null(df_quali.sup)){
gg_graph <- gg_graph + geom_point(aes(x = df_quali.sup[,2], y = df_quali.sup[,3], color = df_quali.sup[,4]), size = ggoptions_default$size/2.8, shape = df_quali.sup[,5])
if (autoLab) text_quali.sup <- ggrepel::geom_text_repel(aes(x = df_quali.sup[,2], y = df_quali.sup[,3], label=df_quali.sup[,1], color = df_quali.sup[,4]), size = ggoptions_default$size, fontface = df_quali.sup[,6])
else{text_quali.sup <- geom_text(aes(x = df_quali.sup[,2], y = df_quali.sup[,3], label=df_quali.sup[,1], color = df_quali.sup[,4]), size = ggoptions_default$size, fontface = df_quali.sup[,6])}
gg_graph <- gg_graph + text_quali.sup
}
gg_graph <- gg_graph + scale_color_gradient(low=ggoptions_default$low.col.quanti, high=ggoptions_default$high.col.quanti) + labs(color = ifelse(legend["title"] %in% legend, legend["title"][[1]], habillage))
}
}
}
if (choix == "quanti.sup") {
gg_graph <- NULL
if (!is.null(res.mca$quanti.sup)) {
if ((new.plot)&!nzchar(Sys.getenv("RSTUDIO_USER_IDENTITY"))) dev.new()
# if (is.null(palette)) palette(c("black","red","green3","blue","cyan","magenta","darkgray","darkgoldenrod","darkgreen","violet","turquoise","orange","lightpink","lavender","yellow","lightgreen","lightgrey","lightblue","darkkhaki", "darkmagenta","darkolivegreen","lightcyan", "darkorange", "darkorchid","darkred","darksalmon","darkseagreen","darkslateblue","darkslategray","darkslategrey","darkturquoise","darkviolet", "lightgray","lightsalmon","lightyellow", "maroon"))
if (is.null(title)) title <- "Supplementary quantitative variables"
if(graph.type=="classic"){
plot(0, 0, main = title, xlab = lab.x, ylab = lab.y, xlim = c(-1.1,1.1), ylim = c(-1.1,1.1), col = "white", asp=1, ...)
abline(v=0,lty=2, ...)
abline(h=0,lty=2, ...)
x.cercle <- seq(-1, 1, by = 0.01)
y.cercle <- sqrt(1 - x.cercle^2)
lines(x.cercle, y = y.cercle,...)
lines(x.cercle, y = -y.cercle,...)
}
if (!is.null(select)) {
if (mode(select)=="numeric") selection <- select
else {
if (sum(rownames(res.mca$quanti.sup$coord)%in%select)!=0) selection <- which(rownames(res.mca$quanti.sup$coord)%in%select)
else {
if (grepl("coord",select)) selection <- (rev(order(apply(res.mca$quanti.sup$coord[,axes]^2,1,sum))))[1:min(nrow(res.mca$quanti.sup$coord),sum(as.integer(unlist(strsplit(select,"coord"))),na.rm=T))]
if (is.integer(select)) selection <- select
}
}
res.mca$quanti.sup$coord <- res.mca$quanti.sup$coord[selection,,drop=FALSE]
}
if(graph.type=="classic"){
for (v in 1:nrow(res.mca$quanti.sup$coord)) {
arrows(0, 0, res.mca$quanti.sup$coord[v, axes[1]], res.mca$quanti.sup$coord[v, axes[2]], length = 0.1, angle = 15, code = 2, col = col.quanti.sup,...)
if (abs(res.mca$quanti.sup$coord[v,axes[1]])>abs(res.mca$quanti.sup$coord[v,axes[2]])){
if (res.mca$quanti.sup$coord[v,axes[1]]>=0) pos<-4
else pos<-2
}
else {
if (res.mca$quanti.sup$coord[v,axes[2]]>=0) pos<-3
else pos<-1
}
if((!is.null(label)) && (label=="all" | "quanti.sup" %in% label)){
text(res.mca$quanti.sup$coord[v, axes[1]], y = res.mca$quanti.sup$coord[v, axes[2]], labels = rownames(res.mca$quanti.sup$coord)[v], pos = pos, col = col.quanti.sup,...)
}
}
}
if(graph.type=="ggplot"){
if (autoLab=="auto") autoLab <- (length(which(rownames(res.mca$quanti.sup$coord)!=""))<50)
df_quanti.sup <- data.frame(rownames(res.mca$quanti.sup$coord),res.mca$quanti.sup$coord[,axes[1]],res.mca$quanti.sup$coord[,axes[2]])
circle <- annotate("path",
x=0+1*cos(seq(0,2*pi,length.out=100)),
y=0+1*sin(seq(0,2*pi,length.out=100)),
lty = ggoptions_default$circle.lty,
lwd = ggoptions_default$circle.lwd,
color = ggoptions_default$circle.color)
gg_graph <- ggplot() +
coord_fixed(ratio = 1) +
geom_line(aes(x=x, y=y), data=data.frame(x=-1:1,y=0),lty=ggoptions_default$line.lty, lwd = ggoptions_default$line.lwd, color=ggoptions_default$line.color) +
geom_line(aes(x=x, y=y), data=data.frame(x=0,y=-1:1),lty=ggoptions_default$line.lty, lwd = ggoptions_default$line.lwd, color=ggoptions_default$line.color) +
theme_light()
if(habillage=="none"){
gg_graph <- gg_graph +
aes(x=df_quanti.sup[,2], y=df_quanti.sup[,3]) +
geom_segment(aes(x=0,y=0,xend=df_quanti.sup[,2], yend=df_quanti.sup[,3]),arrow=arrow(length=unit(0.2,"cm")), lty = ggoptions_default$segment.lty, lwd = ggoptions_default$segment.lwd, color = col.quanti.sup)
if(autoLab) text <- ggrepel::geom_text_repel(aes(x=df_quanti.sup[,2], y=df_quanti.sup[,3],label=df_quanti.sup[,1]), size = ggoptions_default$size, color = col.quanti.sup)
else{text <- geom_text(aes(x=df_quanti.sup[,2], y=df_quanti.sup[,3],label=df_quanti.sup[,1]), size = ggoptions_default$size, color = col.quanti.sup, hjust = (-sign(df_quanti.sup[,2])+1)/2, vjust = -sign(df_quanti.sup[,3])*0.75+0.25)}
}
gg_graph <- gg_graph + text + theme + circle
gg_graph <- gg_graph + xlab(lab.x) + ylab(lab.y) + ggtitle(title)
}
}
}
if (choix == "var") {
lab.var <- lab.quali.sup <- lab.quanti.sup <- FALSE
if(length(label)==1 && label=="all") lab.var <- lab.quali.sup <- lab.quanti.sup <- TRUE
if("var" %in% label) lab.var<-TRUE
if("quali.sup" %in% label) lab.quali.sup<-TRUE
if("quanti.sup" %in% label) lab.quanti.sup<-TRUE
test.invisible <- vector(length = 3)
if (!is.null(invisible)) {
test.invisible[1] <- match("var", invisible)
test.invisible[2] <- match("quali.sup", invisible)
test.invisible[3] <- match("quanti.sup", invisible)
}
else test.invisible <- rep(NA, 3)
if ((new.plot)&!nzchar(Sys.getenv("RSTUDIO_USER_IDENTITY"))) dev.new()
# if (is.null(palette)) palette(c("black","red","green3","blue","cyan","magenta","darkgray","darkgoldenrod","darkgreen","violet","turquoise","orange","lightpink","lavender","yellow","lightgreen","lightgrey","lightblue","darkkhaki", "darkmagenta","darkolivegreen","lightcyan", "darkorange", "darkorchid","darkred","darksalmon","darkseagreen","darkslateblue","darkslategray","darkslategrey","darkturquoise","darkviolet", "lightgray","lightsalmon","lightyellow", "maroon"))
if (is.null(xlim)) xlim <- c(0,1)
if (is.null(ylim)) ylim <- c(0,1)
if (graph.type == "classic"){
plot(0, 0, main = title, xlab = lab.x, ylab = lab.y, xlim = xlim, ylim = ylim, col = "white", asp=1, ...)
abline(v=0,lty=2, ...)
abline(h=0,lty=2, ...)
}
if (is.null(title)) title <- "Variables representation"
coo <- labe <- coll <- ipch <- fonte <- NULL
coord.actif <- res.mca$var$eta2[, axes,drop=FALSE]
if (!is.null(res.mca$quali.sup$eta2)) coord.illu <- res.mca$quali.sup$eta2[,axes,drop=FALSE]
if (!is.null(res.mca$quanti.sup$coord)) coord.illuq <- res.mca$quanti.sup$coord[,axes,drop=FALSE]^2
if (is.na(test.invisible[1])){
coo <- rbind(coo,coord.actif)
if (lab.var){ labe <- c(labe,rownames(coord.actif))
} else labe <- c(labe,rep("",nrow(coord.actif)))
if (length(col.var)==1) coll <- c(coll,rep(col.var,nrow(coord.actif)))
else coll <- col.var
ipch <- c(ipch,rep(20,nrow(coord.actif)))
fonte <- c(fonte,rep(1,nrow(coord.actif)))
}
if ((!is.null(res.mca$quali.sup$eta2))&&(is.na(test.invisible[2]))){
coo <- rbind(coo,coord.illu)
if (lab.quali.sup){ labe <- c(labe,rownames(coord.illu))
} else labe <- c(labe,rep("",nrow(coord.illu)))
if (length(col.quali.sup)==1) coll <- c(coll,rep(col.quali.sup,nrow(coord.illu)))
else coll <- c(coll,col.quali.sup)
ipch <- c(ipch,rep(1,nrow(coord.illu)))
fonte <- c(fonte,rep(3,nrow(coord.illu)))
}
if ((!is.null(res.mca$quanti.sup$coord))&&(is.na(test.invisible[3]))){
coo <- rbind(coo,coord.illuq)
if (lab.quanti.sup){ labe <- c(labe,rownames(coord.illuq))
} else labe <- c(labe,rep("",nrow(coord.illuq)))
if (length(col.quanti.sup)==1) coll <- c(coll,rep(col.quanti.sup,nrow(coord.illuq)))
else coll <- c(coll,col.quanti.sup)
ipch <- c(ipch,rep(1,nrow(coord.illuq)))
fonte <- c(fonte,rep(3,nrow(coord.illuq)))
}
### 22 mars 2018
selection <- NULL
if (!is.null(select)) {
if (mode(select)=="numeric") selection <- (rev(order(apply(coo^2,1,sum))))[1:min(nrow(coo), as.integer(select))]
else {
if (sum(rownames(coo)%in%select)!=0) selection <- which(rownames(coo)%in%select)
else {
if (grepl("coord",select)) selection <- (rev(order(apply(coo^2,1,sum))))[1:min(nrow(coo),sum(as.integer(unlist(strsplit(select,"coord"))),na.rm=T))]
if (is.integer(select)) selection <- select
}
}
}
if (!is.null(select)) {
if (is.numeric(unselect)) coll[!((1:length(coll))%in%selection)] <- rgb(t(col2rgb(coll[!((1:length(coll))%in%selection)])),alpha=255*(1-unselect),maxColorValue=255)
else coll[!((1:length(coll))%in%selection)] <- unselect
labe[!((1:length(labe))%in%selection)] <- ""
}
### Fin 22 mars 2018
if(graph.type== "classic"){
if (any(labe!="")){
if (autoLab=="auto") autoLab <- (length(which(labe!=""))<50)
if (autoLab ==TRUE) autoLab(coo[labe!="", 1], y = coo[labe!="", 2], labels = labe[labe!=""], col = coll[labe!=""], font=fonte[labe!=""],...)
if (autoLab ==FALSE) text(coo[labe!="", 1], y = coo[labe!="", 2], labels = labe[labe!=""], col = coll[labe!=""], font=fonte[labe!=""],pos=3,...)
}
points(coo[, 1], y = coo[, 2], pch = ipch, col = coll, ...)
}
if(graph.type == "ggplot"){
if (autoLab=="auto") autoLab <- (length(which(labe!=""))<50)
df_var <- data.frame(labe,coo,coll,ipch,fonte)
df_var[,5][which(df_var[,5] == 20)] <- 19
gg_graph <- ggplot() +
coord_fixed(ratio = 1) +
xlab(lab.x) + ylab(lab.y) +
xlim(xlim) + ylim(ylim) +
geom_hline(yintercept = 0,lty=ggoptions_default$line.lty, lwd = ggoptions_default$line.lwd, color=ggoptions_default$line.color) +
geom_vline(xintercept = 0,lty=ggoptions_default$line.lty, lwd = ggoptions_default$line.lwd, color=ggoptions_default$line.color) +
theme_light() +
ggoptions_default$theme +
ggtitle(title)
if(habillage == "none"){
gg_graph <- gg_graph + geom_point(aes(x=df_var[,2], y=df_var[,3]), color= df_var[,4], shape = df_var[,5])
if(autoLab) text <- ggrepel::geom_text_repel(aes(x=df_var[,2], y=df_var[,3], label=df_var[,1]), size = ggoptions_default$size, color = df_var[,4], fontface = df_var[,6])
else{text <- geom_text(aes(x=df_var[,2], y=df_var[,3], label=df_var[,1]), size = ggoptions_default$size, color = df_var[,4], hjust = (-sign(df_var[,2])+1)/2, vjust = -sign(df_var[,3])*0.75+0.25, fontface = df_var[,6])}
gg_graph <- gg_graph + text
}
# if(habillage == "cos2"){
# df_ind <- NULL
# if(is.na(test.invisible[1])) df_ind <- rbind(df_ind, df_var[rownames(res.mca$var$eta2), ,drop = FALSE])
# if(is.na(test.invisible[2])) df_ind <- rbind(df_ind, df_var[rownames(res.mca$quali.sup$eta2), ,drop = FALSE])
# #if(is.na(test.invisible[3])) df_ind <- rbind(df_ind, df_var[rownames(res.mca$quanti.sup$coord), ,drop = FALSE])
#
# coll_var <- coll_quali.sup <- coll_quanti.sup <- NULL
# if(!is.null(res.mca$var$cos2) & (is.na(test.invisible[1]))){
# coll_var <- apply(res.mca$var$cos2[,axes,drop = FALSE],1,FUN=sum)}
# if(!is.null(res.mca$quali.sup$cos2) & (is.na(test.invisible[2]))){
# coll_quali.sup <- apply(res.mca$quali.sup$cos2[,axes,drop = FALSE],1,FUN=sum)}
# # if(!is.null(res.mca$quanti.sup$cos2) & (is.na(test.invisible[3]))){
# # coll_quanti.sup <- apply(res.mca$quanti.sup$cos2[,axes,drop = FALSE],1,FUN=sum)}
# coll_quanti <- c(coll_var,coll_quali.sup,coll_quanti.sup)
# #df_ind[,4] <- coll_quanti
#
# gg_graph <- ggplot() +
# coord_fixed(ratio = 1) +
# geom_point(aes(x=df_ind[,2], y=df_ind[,3], color = df_ind[,4]), shape = df_ind[,5]) +
# xlab(lab.x) + ylab(lab.y) +
# xlim(xlim) + ylim(ylim) +
# geom_hline(yintercept = 0,lty=ggoptions_default$line.lty, lwd = ggoptions_default$line.lwd, color=ggoptions_default$line.color) +
# geom_vline(xintercept = 0,lty=ggoptions_default$line.lty, lwd = ggoptions_default$line.lwd, color=ggoptions_default$line.color) +
# scale_color_gradient(low=ggoptions_default$low.col.quanti, high=ggoptions_default$high.col.quanti) +
# labs(color = ifelse(legend["title"] %in% legend, legend["title"][[1]], "cos2")) +
# theme_light() +
# ggoptions_default$theme +
# ggtitle(title)
# if (autoLab) text <- ggrepel::geom_text_repel(aes(x=df_ind[,2], y=df_ind[,3], label=df_ind[,1], color = df_ind[,4]), size = ggoptions_default$size, show.legend = FALSE,fontface=df_ind[,6])
# else{text <- geom_text(aes(x=df_ind[,2], y=df_ind[,3], label=df_ind[,1], color = df_ind[,4]), size = ggoptions_default$size, show.legend = FALSE, nudge_y = nudge_y,fontface=df_ind[,6])}
# gg_graph <- gg_graph + text
# }
# if(habillage == "contrib"){
#
# }
gg_graph <- gg_graph + theme
}
}
palette(old.palette)
if(graph.type == "ggplot") return(gg_graph)
}
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