fviz_famd: Visualize Factor Analysis of Mixed Data

Description

Factor analysis of mixed data (FAMD) is a particular case of MFA, used to analyze a data set containing both quantitative and qualitative variables. fviz_famd() provides ggplot2-based elegant visualization of FAMD outputs from the R function: FAMD [FactoMineR].

fviz_famd_ind(): Graph of individuals
fviz_famd_var(): Graph of variables
fviz_famd(): An alias of fviz_famd_ind(res.famd)

Usage

fviz_famd_ind(
  X,
  axes = c(1, 2),
  geom = c("point", "text"),
  repel = FALSE,
  habillage = "none",
  palette = NULL,
  addEllipses = FALSE,
  col.ind = "blue",
  col.ind.sup = "darkblue",
  alpha.ind = 1,
  shape.ind = 19,
  col.quali.var = "black",
  select.ind = list(name = NULL, cos2 = NULL, contrib = NULL),
  gradient.cols = NULL,
  ...
)
fviz_famd_var(
  X,
  choice = c("var", "quanti.var", "quali.var", "quali.sup"),
  axes = c(1, 2),
  geom = c("point", "text"),
  repel = FALSE,
  col.var = "red",
  alpha.var = 1,
  shape.var = 17,
  col.var.sup = "darkgreen",
  select.var = list(name = NULL, cos2 = NULL, contrib = NULL),
  ...
)
fviz_famd(X, ...)

Value

a ggplot

Arguments

X

an object of class FAMD [FactoMineR].

axes

a numeric vector of length 2 specifying the dimensions to be plotted.

geom

a text specifying the geometry to be used for the graph. Allowed values are the combination of c("point", "arrow", "text"). Use "point" (to show only points); "text" to show only labels; c("point", "text") or c("arrow", "text") to show arrows and texts. Using c("arrow", "text") is sensible only for the graph of variables.

repel

logical; whether to use ggrepel to avoid overplotting text labels. The old jitter argument is kept for backward compatibility and is converted to repel = TRUE with a deprecation warning.

habillage

an optional factor variable for coloring the observations by groups. Default value is "none". If X is a FAMD object from FactoMineR package, habillage can also specify the index of the factor variable in the data.

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.

addEllipses

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

col.ind, col.var

color for individuals and variables, respectively. Can be a continuous variable or a factor variable. Possible values also include "cos2", "contrib", "coord", "x", and "y". In this case, the colors for individuals/variables are automatically controlled by their qualities ("cos2"), contributions ("contrib"), coordinates (x^2 + y^2 , "coord"), x values("x") or y values("y"). To use automatic coloring (by cos2, contrib, ....), make sure that habillage ="none".

col.ind.sup

color for supplementary individuals

alpha.ind, alpha.var

controls the transparency of individuals and variables, respectively. The value can vary from 0 (total transparency) to 1 (no transparency). Default value is 1. Possible values also include "cos2", "contrib", "coord", "x" or "y". In this case, the transparency for individual/variable colors are automatically controlled by their qualities ("cos2"), contributions ("contrib"), coordinates (x^2 + y^2 , "coord"), x values("x") or y values("y"). To use this, make sure that habillage ="none".

shape.ind, shape.var

point shapes of individuals, variables, groups and axes

col.quali.var

color for qualitative variables in fviz_famd_ind(). Default is "black".

select.ind, select.var

a selection of individuals and variables to be drawn. Allowed values are NULL or a list containing the arguments name, cos2 or contrib:

name is a character vector containing individuals/variables to be drawn
cos2 if cos2 is in [0, 1], ex: 0.6, then individuals/variables with a cos2 > 0.6 are drawn. if cos2 > 1, ex: 5, then the top 5 individuals/variables with the highest cos2 are drawn.
contrib if contrib > 1, ex: 5, then the top 5 individuals/variables with the highest contributions are drawn
union: logical. When several of name/cos2/contrib are given, FALSE (default) combines them with AND (each condition further narrows the selection); TRUE combines them with OR (an element is kept if it matches any condition), e.g. named items plus the top-cos2 ones.

gradient.cols

vector of colors to use for n-colour gradient. Allowed values include brewer and ggsci color palettes.

...

Arguments to be passed to the function fviz()

choice

The graph to plot in fviz_famd_var(). Allowed values include one of c("var", "quanti.var", "quali.var", "quali.sup").

col.var.sup

color for supplementary variables.

Author

Alboukadel Kassambara alboukadel.kassambara@gmail.com

Examples

Run this code

# Compute FAMD
 library("FactoMineR")
 data(wine)
 res.famd <- FAMD(wine[,c(1,2, 16, 22, 29, 28, 30,31)], graph = FALSE)
 res.famd.sup <- FAMD(wine[,c(1,2, 16, 22, 29, 28, 30,31)],
                      sup.var = 2, graph = FALSE)
               
# Eigenvalues/variances of dimensions
fviz_screeplot(res.famd)
# Graph of variables
fviz_famd_var(res.famd)
# Quantitative variables
fviz_famd_var(res.famd, "quanti.var", repel = TRUE, col.var = "black")
# Qualitative variables
fviz_famd_var(res.famd, "quali.var", col.var = "black")
# Supplementary qualitative variable categories
fviz_famd_var(res.famd.sup, "quali.sup", col.var = "darkgreen")
# Graph of individuals colored by cos2
fviz_famd_ind(res.famd, col.ind = "cos2", 
  gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"),
  repel = TRUE)