plot.inertia {adegraphics}

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 [e-mail] 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")