Author: Aurélie Siberchicot, Stéphane Dray, Jean Thioulouse
Date: 2025-04-07

# Frequently Asked Questions

#### Aurélie Siberchicot, Stéphane Dray, Jean Thioulouse

#### 2025-04-07

    set.seed(2564)
    library(ade4)
    library(adegraphics)

    ## Registered S3 methods overwritten by 'adegraphics':
    ##   method         from
    ##   biplot.dudi    ade4
    ##   kplot.foucart  ade4
    ##   kplot.mcoa     ade4
    ##   kplot.mfa      ade4
    ##   kplot.pta      ade4
    ##   kplot.sepan    ade4
    ##   kplot.statis   ade4
    ##   scatter.coa    ade4
    ##   scatter.dudi   ade4
    ##   scatter.nipals ade4
    ##   scatter.pco    ade4
    ##   score.acm      ade4
    ##   score.mix      ade4
    ##   score.pca      ade4
    ##   screeplot.dudi ade4

    ##
    ## Attachement du package : 'adegraphics'

    ## Les objets suivants sont masqués depuis 'package:ade4':
    ##
    ##     kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
    ##     s.label, s.logo, s.match, s.traject, s.value, table.value,
    ##     triangle.class

# 1 How to personalize plots

## 1.1 How to update title axes?

    df <- data.frame(x = rep(1:10,1),
                     y = rep(1:10, each = 10),
                     ms_li = runif(100, min = -5, max = 4))
    s.value(df[, 1:2], df$ms_li,
            paxes.draw = TRUE)

### 1.1.1 Size titles on axes

`xlab.cex` and `ylab.cex` manage the size titles on the `x` and `y` axes.

    s.value(df[, 1:2], df$ms_li,
            paxes.draw = TRUE,
            xlab = "Longitude", xlab.cex = 0.5,
            ylab = "Latitude", ylab.cex = 0.5
            )

### 1.1.2 Size labels on axes

`scales.x.cex` and `scales.y.cex` manage the sizes labels on the `x` and `y` axes.

    s.value(df[, 1:2], df$ms_li,
            paxes.draw = TRUE,
            scales.x.cex = 0.5,
            scales.y.cex = 0.5
            )

### 1.1.3 Margin of axis

`layout.heights = list(bottom.padding = 1)` manages the margin of the bottom axis. This enlarges the space for a larger title axis.

    s.value(df[, 1:2], df$ms_li,
            paxes.draw = TRUE,
            xlab = "Longitude", xlab.cex = 2,
            ylab = "Latitude", ylab.cex = 2,
            layout.heights = list(bottom.padding = 2)
            )

## 1.2 How to update label’s boxes ?

    x0 <- runif(50, -2, 2)
    y0 <- runif(50, -2, 2)
    s.label(data.frame(x0, y0))

### 1.2.1 Remove boxes around labels

    s.label(data.frame(x0, y0), plabels.boxes.border = 0)

    s.label(data.frame(x0, y0), plabels.boxes.draw = FALSE, ppoints.cex = 0)

### 1.2.2 Color of label’s boxes

    s.label(data.frame(x0, y0), plabels.boxes.col = "orange")

### 1.2.3 Border of label’s boxes

    s.label(data.frame(x0, y0), plabels.boxes.border = "blue", plabels.boxes.lwd = 2)