# plot.inertia: Display the decomposition of inertia which measure the... In adegraphics: An S4 Lattice-Based Package for the Representation of Multivariate Data

## Description

S3 method to display the decomposition of inertia (`inertia` object) which measure the contributions of rows/columns in mutivariate methods (`dudi` objects from `ade4`)

## Usage

 ```1 2 3 4 5 6 7 8``` ```## S3 method for class 'inertia' plot(x, xax = 1, yax = 2, threshold = 0.1, contrib = c("abs", "rel"), type = c("label", "cross", "ellipse", "both"), ellipseSize = 1.5, posieig = "none", plot = TRUE, storeData = TRUE, pos = -1, ...) ## S3 method for class 'inertia' score(x, xax = 1, threshold = 0.1, contrib = c("abs", "rel"), posieig = "none", pos = -1, storeData = TRUE, plot = TRUE, ...) ```

## Arguments

 `x` an object of the `dudi` class; it must be the output of a correspondance analysis (`coa` object). `xax` an integer indicating which column of x is plotted on the x-axis `yax` an integer indicating which column of x is plotted on the y-axis. If `yax` is equal to `xax`, a one-dimensional graph is display. `threshold` a numeric value containing the contribution threshold (between 0 and 1) at which points should be drawn on the graphic. Low contribution points will be represented by a grey point and without label. When the contributions are displayed on a single axis, a dotted line describes the contribution threshold. `contrib` a character value indicating which contributions are plotted: `abs` for absolute contributions (rows/columns involved in the factor axis/map construction) and `rel` for relative contribution (quality of rows/columns representation on the factor axis/map). `type` a character value indicating which type represents contribution. Labels size (`label`), crosses size(`cross`) or ellipses size (`ellipse`) can be proportional to the contributions. If `type` is `both`, crosses and ellipses both have sizes proportional to the contributions. `ellipseSize` a positive number for ellipse size when `type` is `ellipse` `posieig` a character value or a two-length numeric vector (in normalized parent coordinates `npc` from 0 to 1) or `none` value indicating the position of the eigenvalues bar plot. `plot` a logical indicating if the graphics is displayed `storeData` a logical indicating if the data should be stored in the returned object. If `FALSE`, only the names of the data arguments are stored `pos` an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if `storeData` is `FALSE` `...` additional graphical parameters (see `adegpar` and `trellis.par.get`)

## Value

Returns an `ADEgS` object. The result is displayed if `plot` is `TRUE`.

## Author(s)

Clément Claustre, Anne-Béatrice Dufour, Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stéphane Dray

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47``` ```# First example data(bf88, package = "ade4") coa1 <- ade4::dudi.coa(bf88\$S1, scannf = FALSE, nf = 2) ###### row=T / col=F res11 <- ade4::inertia(coa1, row = TRUE, col = FALSE, nf = 2) g11 <- plot(res11, threshold = 0.06) g12 <- plot(res11, threshold = 0.06, plabels.boxes.draw = TRUE, plines.lwd = 0, light_row.ppoints.cex = 0, posieig = "bottomleft") g13 <- score(res11, threshold = 0.06) names(g13) g14 <- score(res11, xax = 2, threshold = 0.06) ###### row=F / col=T res12 <- ade4::inertia(coa1, row = FALSE, col = TRUE, nf = 2) res12\$col.abs idx <- which(res12\$col.abs[, 1]/100 >= 0.1 | res12\$col.abs[, 2]/100 >= 0.1) rownames(res12\$col.abs[idx, ]) coa1\$co[idx, ] g15 <- plot(res12) g16 <- score(res12, threshold = 0.08) g17 <- score(res12, threshold = 0.07) ######################################## ######################################## # Second example data(housetasks, package = "ade4") coa2 <- ade4::dudi.coa(housetasks, scann = FALSE) ###### row=T / col=F res21 <- ade4::inertia(coa2, row = TRUE, col = FALSE) g21 <- plot(res21) g22 <- score(res21) g23 <- score(res21, xax = 2) ###### row=F / col=T res22 <- ade4::inertia(coa2, row = FALSE, col = TRUE) g24 <- plot(res22, plabels.cex = 2) names(g24) g25 <- plot(res22, posieig = "topleft") names(g25) g26 <- plot(res22, heavy_col.plabels.box.draw = TRUE, light_col.ppoints.col = "purple") g27 <- plot(res22, type = "both") g28 <- plot(res22, type = "ellipse", ellipseSize = 3, plabels.col = "black", pellipse.col = "purple", pellipses.border = "black") ```

### Example output

```Registered S3 methods overwritten by 'adegraphics':
method         from
[1] "light_row"    "heavy_row"    "contribution"
Axis1      Axis2
Pol  0.8743973  5.1626961
Bur  7.8110473 26.3922063
Pro 90.4867942  0.8961601
Cor  0.8277612 67.5489375
[1] "Bur" "Pro" "Cor"
Comp1      Comp2
Bur  0.3532161  0.6219892
Pro -3.0848713  0.2941009
Cor  0.1552816 -1.3438037
[1] "light_col" "heavy_col"
[1] "light_col" "heavy_col" "eig"
```

adegraphics documentation built on Sept. 16, 2021, 5:07 p.m.