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

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

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 = 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")
#> Error in plot.inertia(res11, threshold = 0.06, plabels.boxes.draw = TRUE,     plines.lwd = 0, light_row.ppoints.cex = 0, posieig = "bottomleft"): object 'coa1' not found
g13 <- score(res11, threshold = 0.06)

names(g13)
#> [1] "light_row"    "heavy_row"    "contribution"
g14 <- score(res11, xax = 2, threshold = 0.06)


###### row=F / col=T
res12 <- ade4::inertia(coa1, row = FALSE, col = TRUE, nf = 2)
res12$col.abs
#>          Axis1      Axis2       Axis3
#> Pol  0.8743973  5.1626961 90.27575579
#> Bur  7.8110473 26.3922063  9.14870165
#> Pro 90.4867942  0.8961601  0.01369376
#> Cor  0.8277612 67.5489375  0.56184880
idx <- which(res12$col.abs[, 1]/100 >= 0.1 | res12$col.abs[, 2]/100 >= 0.1)
rownames(res12$col.abs[idx, ])
#> [1] "Bur" "Pro" "Cor"
coa1$co[idx, ]
#>          Comp1      Comp2       Comp3
#> Bur  0.3532161  0.6219892 -0.30249951
#> Pro -3.0848713  0.2941009  0.03003066
#> Cor  0.1552816 -1.3438037  0.10123630
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)
#> [1] "light_col" "heavy_col"
g25 <- plot(res22, posieig = "topleft")
#> Error in plot.inertia(res22, posieig = "topleft"): object 'coa2' not found
names(g25)
#> Error in eval(expr, envir, enclos): object 'g25' not found
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")