README.md

title: "README.md" author: - Philip D. Waggoner^[University of Chicago] - Fong Chun Chan^[Achilles Therapeutics] - Lu Zhang^[Emory University] date: 07/08/2020 output: html_document

In collaboration with Fong Chan (Achilles Therapeutics) and Lu Zhang (Emory University), we have developed plotmm for tidy visualization of mixture models. This package is a substantial update to the plotGMM package.

The package has five functions:

  1. plot_mm(): The main function of the package, plot_mm allows the user to simply input the name of the fit mixture model, as well as an optional argument to pass the number of components k that were used in the original fit. Note: the function will automatically detect the number of components if k is not supplied. The result is a tidy ggplot of the density of the data with overlaid mixture weight component curves. Importantly, as the grammar of graphics is the basis of visualization in this package, all other tidyverse-friendly customization options work with any of the plotmm's functions (e.g., customizing with ggplot2's functions like labs() or theme_*(); or patchwork's plot_annotation()). There are examples of these and others below.

  2. plot_cut_point(): Mixture models are often used to derive cut points of separation between groups in feature space. plot_cut_point() plots the data density with the overlaid cut point (the mean of the calculated mu) from the fit mixture model.

  3. plot_mix_comps(): A helper function allowing for expanded customization of mixture model plots. The function superimposes the shape of the components over a ggplot2 object. This function is also used to render all plots in the main plot_mm() function.

  4. plot_gmm(): The original function upon which the package was expanded. It is included in plotmm for quicker access to a common mixture model form (univariate Gaussian), as well as to bridge between the original plotGMM package.

  5. plot_mix_comps_normal(): Similarly, this function is the original basis of plot_mix_comps(), but for Gaussian mixture models only. It is included in plotmm for bridging between the original plotGMM package.

The package supports several model objects (from 'mixtools', 'EMCluster', and 'flexmix'), as well as many mixture model specifications, including mixtures of:

  1. Univariate Gaussians
  2. Bivariate Gaussians
  3. Gammas
  4. Logistic regressions
  5. Linear regressions
  6. Poisson regressions

Tidy visualization of mixture models via plot_mm()

First, here is an example for univariate normal mixture model:

set.seed(576)

mixmdl <- mixtools::normalmixEM(iris$Petal.Length, k = 2)

# visualize
plot_mm(mixmdl, 2) +
  ggplot2::labs(title = "Univariate Gaussian Mixture Model",
                subtitle = "Mixtools Object")

Next is an example for a mixture of binary logistic regressions:

# set up the data (replication of mixtools examples for comparability)
beta <- matrix(c(-10, .1, 20, -.1), 2, 2)
x <- runif(500, 50, 250)
x1 <- cbind(1, x)
xbeta <- x1%*%beta
w <- rbinom(500, 1, .3)
y <- w*rbinom(500, size=1, prob=(1/(1+exp(-xbeta[, 1])))) + (1-w)*rbinom(500, size=1, prob=(1/(1+exp(-xbeta[, 2]))))
out <- logisregmixEM(y, x, beta = beta, lambda = c(.3, .7), verb = TRUE, epsilon = 1e-01)

# visualize
plot_mm(out) +
  ggplot2::labs(title = "Mixture of Logistic Regressions",
                subtitle = "Mixtools Object")

Next is an example of a mixture of linear regressions:

# set up the data (replication of mixtools examples for comparability)
data(NOdata)
attach(NOdata)
set.seed(100)
out <- regmixEM(Equivalence, NO, verb = TRUE, epsilon = 1e-04)
df <- data.frame(out$beta)

# visualize
plot_mm(out) +
  ggplot2::labs(title = "Mixture of Regressions",
                subtitle = "Mixtools Object")

Next is a bivariate Gaussian mixture model (via EMCluster)

library(EMCluster)
set.seed(1234)
x <- da1$da
out <- init.EM(x, nclass = 10, method = "em.EM")

plot1 <- plot_mm(out, data=x)

plot1 + patchwork::plot_annotation(title = "Bivariate Gaussian Mixture Model",
                                  subtitle = "EMCluster Object")

Plot cut points (or not) via plot_cut_point() (with the amerika color palette)

mixmdl <- mixtools::normalmixEM(faithful$waiting, k = 2)

plot_cut_point(mixmdl, plot = TRUE, color = "amerika") # produces plot

plot_cut_point(mixmdl, plot = FALSE) # gives the cut point value, not the plot

Customize a ggplot with plot_mix_comps()

library(plotGMM)
library(magrittr)
library(ggplot2)

# Fit a univariate mixture model via mixtools
set.seed(576)
mixmdl <- mixtools::normalmixEM(faithful$waiting, k = 2)

# Customize a plot with `plot_mix_comps()`
data.frame(x = mixmdl$x) %>%
ggplot() +
geom_histogram(aes(x, ..density..), binwidth = 1, colour = "black",
                 fill = "white") +
   stat_function(geom = "line", fun = plot_mix_comps, # here is the function
                 args = list(mixmdl$mu[1], mixmdl$sigma[1], lam = mixmdl$lambda[1]),
                 colour = "red", lwd = 1.5) +
   stat_function(geom = "line", fun = plot_mix_comps, # and here again because k = 2
                 args = list(mixmdl$mu[2], mixmdl$sigma[2], lam = mixmdl$lambda[2]),
                 colour = "blue", lwd = 1.5) +
   ylab("Density")


Try the plotmm package in your browser

Any scripts or data that you put into this service are public.

plotmm documentation built on July 10, 2020, 9:06 a.m.