adegraphics: plot.inertia – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

plot.inertia

Display the decomposition of inertia which measure the contributions of rows/columns in mutivariate methods

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

## 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

# 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")

adegraphics

An S4 Lattice-Based Package for the Representation of Multivariate Data

v1.0-15

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr> and Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>, with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferrière.

Initial release

2018-12-18