batchmix workflow

Stephen Coleman

Introduction

This document shows the basics of applying our Bayesian model-based clustering/classification with joint batch correction in R. It shows how to generate some toy data, apply the model, assess convergence and process outputs.

Data generation

We simulate some data using the generateBatchData function.

library(ggplot2)
## Warning: package 'ggplot2' was built under R version 4.3.3
library(batchmix)

# Data dimensions
N <- 600
P <- 4
K <- 5
B <- 7

# Generating model parameters
mean_dist <- 2.25
batch_dist <- 0.3
group_means <- seq(1, K) * mean_dist
batch_shift <- rnorm(B, mean = batch_dist, sd = batch_dist)
std_dev <- rep(2, K)
batch_var <- rep(1.2, B)
group_weights <- rep(1 / K, K)
batch_weights <- rep(1 / B, B)
dfs <- c(4, 7, 15, 60, 120)

my_data <- generateBatchData(
  N,
  P,
  group_means,
  std_dev,
  batch_shift,
  batch_var,
  group_weights,
  batch_weights,
  type = "MVT",
  group_dfs = dfs
)

This gives us a named list with two related datasets, the observed_data which includes batch effects and the corrected_data which is batch-free. It also includes group_IDs, a vector indicating class membership for each item, batch_IDs, which indicates batch of origin for each item, and fixed, which indicates which labels are observed and fixed in the model. We pull these out of the names list in the format that the modelling functions desire them.

X <- my_data$observed_data

true_labels <- my_data$group_IDs
fixed <- my_data$fixed
batch_vec <- my_data$batch_IDs

alpha <- 1
initial_labels <- generateInitialLabels(alpha, K, fixed, true_labels)

Modelling

Given some data, we are interested in modelling it. We assume here that the set of observed labels includes at least one example of each class in the data.

# Sampling parameters
R <- 1000
thin <- 50
n_chains <- 4

# Density choice
type <- "MVT"

# MCMC samples and BIC vector
mcmc_output <- runMCMCChains(
  X,
  n_chains,
  R,
  thin,
  batch_vec,
  type,
  initial_labels = initial_labels,
  fixed = fixed
)

We want to assess two things. First, how frequently the proposed parameters in the Metropolis-Hastings step are accepted:

plotAcceptanceRates(mcmc_output)

Secondly, we want to asses how well our chains have converged. To do this we plot the complete_likelihood of each chain. This is the quantity most relevant to a clustering/classification, being dependent on the labels. The observed_likelihood is independent of labels and more relevant for density estimation.

plotLikelihoods(mcmc_output)

We see that our chains disagree. We have to run them for more iterations. We use the continueChains function for this.

R_new <- 9000

# Given an initial value for the parameters
new_output <- continueChains(
  mcmc_output,
  X,
  fixed,
  batch_vec,
  R_new,
  keep_old_samples = TRUE
)

To see if the chains better agree we re-plot the likelihood.

plotLikelihoods(new_output)

We also re-check the acceptance rates.

plotAcceptanceRates(new_output)

This looks like several of the chains agree by the 5,000th iteration.

Process chains

We process the chains, acquiring point estimates of different quantities.

# Burn in
burn <- 5000

# Process the MCMC samples
processed_samples <- processMCMCChains(new_output, burn)

Visualisation

For multidimensional data we use a PCA plot.

chain_used <- processed_samples[[1]]

pc <- prcomp(X, scale = T)
pc_batch_corrected <- prcomp(chain_used$inferred_dataset)

plot_df <- data.frame(
  PC1 = pc$x[, 1],
  PC2 = pc$x[, 2],
  PC1_bf = pc_batch_corrected$x[, 1],
  PC2_bf = pc_batch_corrected$x[, 2],
  pred_labels = factor(chain_used$pred),
  true_labels = factor(true_labels),
  prob = chain_used$prob,
  batch = factor(batch_vec)
)

plot_df |>
  ggplot(aes(
    x = PC1,
    y = PC2,
    colour = true_labels,
    alpha = prob
  )) +
  geom_point()

plot_df |>
  ggplot(aes(
    x = PC1_bf,
    y = PC2_bf,
    colour = pred_labels,
    alpha = prob
  )) +
  geom_point()

test_inds <- which(fixed == 0)

sum(true_labels[test_inds] == chain_used$pred[test_inds]) / length(test_inds)
## [1] 0.8085106