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Plot Model-Based Clustering Results using ggplot2

Source: R/fviz_mclust.R
fviz_mclust.Rd

Plots the classification, the uncertainty and the BIC values returned by the Mclust() function. Read more: Model-Based Clustering in R (Mclust).

Usage

fviz_mclust(
  object,
  what = c("classification", "uncertainty", "BIC"),
  ellipse.type = "norm",
  ellipse.level = 0.4,
  ggtheme = theme_classic(),
  ...
)

fviz_mclust_bic(
  object,
  model.names = NULL,
  shape = 19,
  color = "model",
  palette = NULL,
  legend = NULL,
  main = "Model selection",
  xlab = "Number of components",
  ylab = "BIC",
  ...
)

Arguments

object

an object of class Mclust

what

choose from one of the following three options: "classification" (default), "uncertainty" and "BIC".

ellipse.type

Character specifying frame type. Possible values are 'convex', 'confidence' or types supported by stat_ellipse including one of c("t", "norm", "euclid").

ellipse.level

the size of the concentration ellipse in normal probability. Passed for ggplot2::stat_ellipse 's level. Ignored in 'convex'. Default value is 0.95.

ggtheme

function, ggplot2 theme name. The default is set by each function's ggtheme argument; see the function usage for the actual default. Set ggtheme = NULL to skip applying a ggpubr theme, so the plot keeps ggplot2 default theme or the theme set globally via theme_set(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

...

other arguments to be passed to the functions fviz_cluster and ggpar.

model.names

one or more model names corresponding to models fit in object. The default is to plot the BIC for all of the models fit.

shape

point shape. To change point shape by model names use shape = "model".

color

point and line color.

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.

legend

character specifying legend position. Allowed values are one of c("top", "bottom", "left", "right", "none"). To remove the legend use legend = "none". Legend position can be also specified using a numeric vector c(x, y); see details section.

main

plot main title.

xlab

character vector specifying x axis labels. Use xlab = FALSE to hide xlab.

ylab

character vector specifying y axis labels. Use ylab = FALSE to hide ylab.

Value

A ggplot2 object.

Functions

  • fviz_mclust(): Plots classification and uncertainty.

  • fviz_mclust_bic(): Plots the BIC values.

See also

fviz_cluster. Online tutorial: Model-Based Clustering in R (Mclust).

Examples


if(requireNamespace("mclust", quietly = TRUE)){

# Compute model-based-clustering
library("mclust")
data("diabetes")
mc <- Mclust(diabetes[, -1])

# Visualize BIC values
fviz_mclust_bic(mc)

# Visualize classification
fviz_mclust(mc, "classification", geom = "point")
}
#> Package 'mclust' version 6.1.2
#> Type 'citation("mclust")' for citing this R package in publications.
#> 
#> Attaching package: ‘mclust’
#> The following object is masked from ‘package:dplyr’:
#> 
#>     count