metasnf

Scalable subtyping with similarity network fusion

https://github.com/branchlab/metasnf

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Scalable subtyping with similarity network fusion

README.Rmd

---
output: github_document
bibliography: bibliography.bib
link-citations: yes
linkcolor: blue
---



```{r, include = FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)
```

# metaSNF: Meta clustering with Similarity Network Fusion




## Brief Overview

metaSNF is an R package that facilitates usage of the meta clustering paradigm described in [@caruanaMeta2006] with the similarity network fusion (SNF) data integration procedure developed in [@wangSimilarity2014].
The package offers a comprehensive suite of tools to assist users in transforming multi-modal tabular data into cluster solutions, decision making in the clustering process, and visualization along the way with a strong emphasis on context-specific utility and principled validation of results.

## Installation

You will need R version 4.1.0 or higher to install this package.
metaSNF can be installed from CRAN:

```{r eval = FALSE}
install.packages("metasnf")
```

Development versions can be installed from GitHub:

```{r eval = FALSE}
# Latest development version
devtools::install_github("BRANCHlab/metasnf")

# Install a specific tagged version
devtools::install_github("BRANCHlab/metasnf@v2.1.3")
```

## Quick Start

Minimal usage of the package looks like this:

```{r}
# Load the package
library(metasnf)

# Setting up the data
dl <- data_list(
    list(abcd_cort_t, "cortical_thickness", "neuroimaging", "continuous"),
    list(abcd_cort_sa, "cortical_surface_area", "neuroimaging", "continuous"),
    list(abcd_subc_v, "subcortical_volume", "neuroimaging", "continuous"),
    list(abcd_income, "household_income", "demographics", "continuous"),
    list(abcd_pubertal, "pubertal_status", "demographics", "continuous"),
    uid = "patient"
)

# Specifying 5 different sets of settings for SNF
set.seed(42)
sc <- snf_config(
    dl,
    n_solutions = 5,
    max_k = 40
)

# This matrix has clustering solutions for each of the 5 SNF runs!
sol_df <- batch_snf(dl, sc)

sol_df

t(sol_df)
```

Check out the tutorial vignettes below to learn about how the package can be used:

* [Simple usage of the package](https://branchlab.github.io/metasnf/articles/a_simple_example.html)
* [Complex usage of the package](https://branchlab.github.io/metasnf/articles/a_complete_example.html)

And more tutorials can be found under the "articles" section of the documentation home page: [https://branchlab.github.io/metasnf/index.html](https://branchlab.github.io/metasnf/index.html)


## Background

**Why use meta clustering?**

Clustering algorithms seek solutions where members of the same cluster are very similar to each other and members of distinct clusters are very dissimilar to each other.
In sufficiently noisy datasets where many qualitatively distinct solutions with similar scores of clustering quality exist, it is not necessarily the case that the top solution selected by a clustering algorithm will also be the most useful one for the user's context.

To address this issue, the original meta clustering procedure [Caruana et al., 2006](https://doi.org/10.1109/ICDM.2006.103) involved generating a large number of reasonable clustering solutions, clustering those solutions into qualitatively similar ones, and having the user examine those "meta clusters" to find something that seems like it'll be the most useful.

**Why use SNF?**

In the clinical data setting, we often have access to patient data across a wide range of domains, such as imaging, genetics, biomarkers, demographics.
When trying to extract subtypes out of all this information, direct concatenation of the data followed by cluster analysis can result in a substantial amount of lost (valuable) signal contained in each individual domain.
Empirically, SNF has been demonstrated to effectively integrate highly diverse patient data for the purposes of clinical subtyping.

## Documentation

### Example workflows

* [Simple](https://branchlab.github.io/metasnf/articles/a_simple_example.html)
* [Complex](https://branchlab.github.io/metasnf/articles/a_complete_example.html)

### Essential objects

* [SNF config](https://branchlab.github.io/metasnf/articles/snf_config.html)
* [Data list](https://branchlab.github.io/metasnf/articles/data_list.html)

### Further customization of generated solutions

* [SNF schemes](https://branchlab.github.io/metasnf/articles/snf_schemes.html)
* [Distance metrics](https://branchlab.github.io/metasnf/articles/distance_metrics.html)
* [Clustering algorithms](https://branchlab.github.io/metasnf/articles/clustering_algorithms.html)
* [Feature weighting](https://branchlab.github.io/metasnf/articles/feature_weights.html)

### Additional functionality

* [Stability measures and consensus clustering](https://branchlab.github.io/metasnf/articles/stability_measures.html)
* [Removing unwanted signal](https://branchlab.github.io/metasnf/articles/confounders.html)
* [Parallel processing](https://branchlab.github.io/metasnf/articles/parallel_processing.html)
* [Label propagation](https://branchlab.github.io/metasnf/articles/label_propagation.html)
* [Imputations](https://branchlab.github.io/metasnf/articles/imputations.html)
* [NMI scores](https://branchlab.github.io/metasnf/articles/nmi_scores.html)

### Plotting

* [Correlation plots](https://branchlab.github.io/metasnf/articles/correlation_plots.html)
* [Similarity matrix heatmaps](https://branchlab.github.io/metasnf/articles/similarity_matrix_heatmap.html)
* [Manhattan plots](https://branchlab.github.io/metasnf/articles/manhattan_plots.html)
* [Alluvial plots](https://branchlab.github.io/metasnf/articles/alluvial_plots.html)
* [Feature plots](https://branchlab.github.io/metasnf/articles/feature_plots.html)

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