LDA ordination with feature loadings computation

[thpralas]

This PR adds two new methods getLDA and addLDA that perform Latent Dirichlet Allocation.

getLDA returns the ordination matrix with the feature loadings matrix stored as attribute.
addLDA adds this ordination matrix to reducedDims of the TreeSummarizedExperiment.

This PR is related to issue #596.

[antagomir]

Great! I will be first looking fwd to comments from @TuomasBorman and then let's see if I have anything to add.

[antagomir]

Conflicts to resolve?

[TuomasBorman]

Looks good. Even though the code is rather short, structure it by adding tests and comments

[TuomasBorman]

Couple things to discuss:

1. LDA has features from both ordination and clustering methods, however, it is more clustering method. That should be taken into account in documentation.
2. As this is clustering method, should we add clusters to rowData/colData? In theory, LDA can be applied also to rows, which makes reducedDim not suitable for storing the result. (Instead of ordination methods, addCluster() should be used as an example)
3. And finally, should this be implemented in bluster package (the Bioconductor clustering package)? We could make a PR as we did last year https://github.com/LTLA/bluster/blob/master/R/DmmParam.R

[antagomir]

Intuitively, reducedDim is a logical place given that this would be usually done for samples. But it could be in principle applied on both rows and columns. The function generates both feature matrix and feature loading matrix, both should be stored.

LDA is a matrix decomposition method, and I would not recommend to link it with clustering so directly.

But it could in principle go to the bluster package. Not sure if they would approve but it could be asked by opening an issue. That might take more time, however.. therefore I would meanwhile proceed with implementing these in mia, and later we can move them elsewhere if necessary? LDA and NMF have clear uses, it would be useful to have them easily accessible.

[TuomasBorman]

With these explanations, I am fine with mia implementation and reducedDim()

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R/addLDA.R	89.65%	3 Missing ⚠️

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[TuomasBorman]

Minor things

[antagomir]

Ok to me to add that.

However, if it feels a lot to add now, I would focus on finalizing the present one (with a single fixed k) first, and then adding that multi-k optimization as a separate PR.

[TuomasBorman]

That would require something like this

addLDA <- function(eval.metric = "perplexity"){
    if(eval.metric == "coherence" && !require("topicdoc") ){
        stop("'topicmodel' package must be installed in order to calculate coherence.")
    }
    models <- lapply(k, function(x){
        LDA(k = x)
    }
    
    metric <- .calc_metrics(models)
    
    # Get the model with lowest eval.metric (dfault value perplexity).
    
    # Get scores
    # Add loadings, model, and metrics data.frame to attributes

}

.calc_metrics <- function(x){
    # Loop through models
    # Calculate perplexity with topicmodels
    # Calculate coherence (I believe you have to use topicdoc package). Calculate it if that package is available
    # Create df from both metrics
}

[TuomasBorman]

NMF would go with this same template I think. However, there k (rank) can be numeric vector and the function finds optimal k by itself

[TuomasBorman]

For LDA we could have another PR for multiple k values, if you are not able to implement it now

The idea was this:

data("GlobalPatterns")
tse <- GlobalPatterns
tse <- agglomerateByPrevalence(tse, rank="Phylum")

eval.metric <- "perplexity"
k <- c(2, 3, 4, 5, 6, 7, 8, 9, 10)
k <- 5
assay.type <- "counts"

mat <- assay(tse, assay.type)

df <- as.data.frame(t(mat))




if( eval.metric == "coherence" ){
    .require_package("topicdoc")
}

models <- lapply(k, function(i){
    topicmodels::LDA(df, i)
})

metrics <- .calculate_lda_metrics(models, k)

lda_model <- models[[ which.max(metrics[[eval.metric]]) ]]

posteriors <- topicmodels::posterior(lda_model, df)
scores <- t(as.data.frame(posteriors$topics))
attr(scores, "loadings") <- loadings
attr(scores, "model") <- lda_model
attr(scores, "eval_metric") <- metrics 

.calculate_lda_metrics <- function(models, k){
    metrics <- lapply(models, function(model){
        res <- topicmodels::perplexity(model)
        names(res) <- "perplexity"
        if( require("topicdoc") ){
            coherence <- topicdoc::topic_coherence(model, df)
            names(coherence) <- paste0("coherence_", seq_len(length(coherence)))
            coherence <- c(coherence, coherence_mean = mean(coherence))
            res <- c(res, coherence)
        }
        return(res)
    })
    metrics <- as.data.frame( dplyr::bind_rows(metrics) )
    metrics[["k"]] <- k
    return(metrics)
}

#################################
df <- attr(scores, "eval_metric")

library(ggplot2)

ggplot(df) +
    geom_point(aes(x = k, y = perplexity), color = "red")
ggplot(df) +
    geom_point(aes(x = k, y = mean_coherence), color = "blue")

[TuomasBorman]

Is this PR ready? If the modification on multiple k values do not come to this PR, I think this is good to go