R: Visualize Factor Analysis of Mixed Data

fviz_famd {factoextra} | R Documentation

## 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"), 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, ...)

### 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` | a boolean, whether to use ggrepel to avoid overplotting text labels or not.
`habillage` | an optional factor variable for coloring the observations by groups. Default value is "none". If X is an MFA 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 include also : "cos2", "contrib", "coord", "x" or "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 variate from 0 (total transparency) to 1 (no transparency). Default value is 1. Possible values include also : "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_mfa_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 cos2 are drawn
`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 inf fviz_mfa_var(). Allowed values include one of c("var", quanti.var", "quali.var").
`col.var.sup` | color for supplementary variables.

### Value

a ggplot

### Author(s)

Alboukadel Kassambara alboukadel.kassambara@gmail.com

### Examples

    # Compute FAMD
     library("FactoMineR")
     data(wine)
     res.famd <- FAMD(wine[,c(1,2, 16, 22, 29, 28, 30,31)], 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")
    # Graph of individuals colored by cos2
    fviz_famd_ind(res.famd, col.ind = "cos2",
      gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"),
      repel = TRUE)

[Package factoextra version 1.0.5 Index]