Draw confidence ellipses around the categories

Source: R/fviz_ellipses.R

Draw confidence ellipses around the categories

fviz_ellipses(
  X,
  habillage,
  axes = c(1, 2),
  addEllipses = TRUE,
  ellipse.type = "confidence",
  palette = NULL,
  pointsize = 1,
  geom = c("point", "text"),
  ggtheme = theme_bw(),
  ...
)

Arguments

X

an object of class MCA, PCA or MFA.

habillage

a numeric vector of indexes of variables or a character vector of names of variables. Can be also a data frame containing grouping variables.

axes

a numeric vector specifying the axes of interest. Default values are 1:2 for axes 1 and 2.

addEllipses

logical value. If TRUE, draws ellipses around the individuals when habillage != "none".

ellipse.type

Character specifying frame type. Possible values are "convex", "confidence" or types supported by stat_ellipse() including one of c("t", "norm", "euclid") for plotting concentration ellipses.

  • "convex": plot convex hull of a set of points.

  • "confidence": plot confidence ellipses around group mean points as coord.ellipse()[in FactoMineR].

  • "t": assumes a multivariate t-distribution.

  • "norm": assumes a multivariate normal distribution.

  • "euclid": draws a circle with the radius equal to level, representing the euclidean distance from the center. This ellipse probably won't appear circular unless coord_fixed() is applied.

palette

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty". Can be also a numeric vector of length(groups); in this case a basic color palette is created using the function palette.

pointsize

the size of points

geom

a text specifying the geometry to be used for the graph. Allowed values are the combination of c("point", "text"). Use "point" (to show only points); "text" to show only labels; c("point", "text") to show both types.

ggtheme

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

...

Arguments to be passed to the functions ggpubr::ggscatter() & ggpubr::ggpar().

Value

a ggplot

Author

Alboukadel Kassambara alboukadel.kassambara@gmail.com

Examples

# \donttest{

# Multiple Correspondence Analysis
# +++++++++++++++++++++++++++++++++
library(FactoMineR)
data(poison)
res.mca <- MCA(poison, quanti.sup = 1:2, 
              quali.sup = 3:4, graph=FALSE)
              
fviz_ellipses(res.mca, 1:4, geom = "point",
palette = "jco") 
#> Warning: Computation failed in `stat_conf_ellipse()`.
#> Caused by error in `if (scale[1] > 0) ...`:
#> ! missing value where TRUE/FALSE needed
#> Warning: Computation failed in `stat_conf_ellipse()`.
#> Caused by error in `if (scale[1] > 0) ...`:
#> ! missing value where TRUE/FALSE needed
#> Warning: This manual palette can handle a maximum of 10 values. You have supplied 32
#> Warning: Removed 144 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 22 rows containing missing values or values outside the scale range
#> (`geom_point()`).


 # }