| fviz_hmfa {factoextra} | R Documentation |
Visualize Hierarchical Multiple Factor Analysis
Description
Hierarchical Multiple Factor Analysis (HMFA) is, an extension of
MFA, used in a situation where the data are organized into a hierarchical
structure. fviz_hmfa() provides ggplot2-based elegant visualization of HMFA
outputs from the R function: HMFA [FactoMineR].
fviz_hmfa_ind(): Graph of individuals
fviz_hmfa_var(): Graph of variables
fviz_hmfa_quali_biplot(): Biplot of individuals and qualitative variables
fviz_hmfa(): An alias of fviz_hmfa_ind()
Usage
fviz_hmfa_ind(
X,
axes = c(1, 2),
geom = c("point", "text"),
repel = FALSE,
habillage = "none",
addEllipses = FALSE,
shape.ind = 19,
col.ind = "blue",
col.ind.sup = "darkblue",
alpha.ind = 1,
select.ind = list(name = NULL, cos2 = NULL, contrib = NULL),
partial = NULL,
col.partial = "group",
group.names = NULL,
node.level = 1,
...
)
fviz_hmfa_var(
X,
choice = c("quanti.var", "quali.var", "group"),
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_hmfa_quali_biplot(
X,
axes = c(1, 2),
geom = c("point", "text"),
repel = FALSE,
habillage = "none",
title = "Biplot of individuals and qualitative variables - HMFA",
...
)
fviz_hmfa(X, ...)
Arguments
X |
an object of class HMFA [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 |
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 HMFA object from FactoMineR package, habillage can also specify the index of the factor variable in the data. |
addEllipses |
logical value. If TRUE, draws ellipses around the individuals when habillage != "none". |
shape.ind, shape.var |
point shapes of individuals and variables, respectively. |
col.ind, col.var |
color for individuals, partial 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 individual, partial individual and variable, 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". |
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:
|
partial |
list of the individuals for which the partial points should be drawn. (by default, partial = NULL and no partial points are drawn). Use partial = "All" to visualize partial points for all individuals. |
col.partial |
color for partial individuals. By default, points are colored according to the groups. |
group.names |
a vector containing the name of the groups (by default, NULL and the group are named group.1, group.2 and so on). |
node.level |
a single number indicating the HMFA node level to plot. |
... |
Arguments to be passed to the function fviz() and ggpubr::ggpar() |
choice |
the graph to plot. Allowed values include one of c("quanti.var", "quali.var", "group") for plotting quantitative variables, qualitative variables and group of variables, respectively. |
col.var.sup |
color for supplementary variables. |
title |
the title of the graph |
Value
a ggplot
Author(s)
Fabian Mundt f.mundt@inventionate.de
Alboukadel Kassambara alboukadel.kassambara@gmail.com
References
http://www.sthda.com/english/
Examples
# Hierarchical Multiple Factor Analysis
# ++++++++++++++++++++++++
# Install and load FactoMineR to compute MFA
# install.packages("FactoMineR")
library("FactoMineR")
data(wine)
hierar <- list(c(2,5,3,10,9,2), c(4,2))
res.hmfa <- HMFA(wine, H = hierar, type=c("n",rep("s",5)), graph = FALSE)
# Graph of individuals
# ++++++++++++++++++++
# Color of individuals: col.ind = "#2E9FDF"
# Use repel = TRUE to avoid overplotting (slow if many points)
fviz_hmfa_ind(res.hmfa, repel = TRUE, col.ind = "#2E9FDF")
# Color individuals by groups, add concentration ellipses
# Remove labels: label = "none".
# Change color palette to "jco". See ?ggpubr::ggpar
grp <- as.factor(wine[,1])
p <- fviz_hmfa_ind(res.hmfa, label="none", habillage=grp,
addEllipses=TRUE, palette = "jco")
print(p)
# Graph of variables
# ++++++++++++++++++++++++++++++++++++++++
# Quantitative variables
fviz_hmfa_var(res.hmfa, "quanti.var")
# Graph of categorical variable categories
fviz_hmfa_var(res.hmfa, "quali.var")
# Groups of variables (correlation square)
fviz_hmfa_var(res.hmfa, "group")
# Biplot of categorical variable categories and individuals
# +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
fviz_hmfa_quali_biplot(res.hmfa)
# Graph of partial individuals (starplot)
# +++++++++++++++++++++++++++++++++++++++
fviz_hmfa_ind(res.hmfa, partial = "all", palette = "Dark2")