S3 method to display the decomposition of inertia (inertia object)
which measure the contributions of rows/columns in mutivariate methods
(dudi objects from ade4)
# S3 method for 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 inertia
score(x, xax = 1, threshold = 0.1, contrib = c("abs", "rel"),
posieig = "none", pos = -1, storeData = TRUE, plot = TRUE, ...)Returns an ADEgS object.
The result is displayed if plot is TRUE.
an object of the dudi class; it must be the output of a
correspondance analysis (coa object).
an integer indicating which column of x is plotted on the x-axis
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.
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.
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).
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.
a positive number for ellipse size when type is
ellipse
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.
a logical indicating if the graphics is displayed
a logical indicating if the data should be stored in
the returned object. If FALSE, only the names of the data
arguments are stored
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)
Clément Claustre, Anne-Béatrice Dufour, Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stéphane Dray
# First example
data(bf88, package = "ade4")
coa1 <- ade4::dudi.coa(bf88$S1, scannf = FALSE, nf = 3)
###### row=T / col=F
res11 <- ade4::inertia(coa1, row = TRUE, col = FALSE, nf = 3)
g111 <- plot(res11, threshold = 0.06)
g112 <- plot(res11, threshold = 0.06, xax = 1, yax = 3)
g12 <- plot(res11, threshold = 0.06, plabels.boxes.draw = TRUE, plines.lwd = 0,
light_row.ppoints.cex = 0, posieig = "bottomleft")
g13 <- score(res11, threshold = 0.06)
names(g13)
g14 <- score(res11, xax = 2, threshold = 0.06)
###### row=F / col=T
res12 <- ade4::inertia(coa1, row = FALSE, col = TRUE, nf = 2)
res12$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")
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