Dataset Information

Relative density clouds: Visualizing and exploring multivariate patterns of group differences.

ABSTRACT: This paper introduces relative density clouds, a simple but powerful method to visualize the relative density of two groups in multivariate space. Relative density clouds employ k-nearest neighbor density estimates to provide information about group differences throughout the entire distribution of the variables. The method can also be used to decompose overall group differences into the specific contributions of differences in location, scale, and covariation. Existing relative distribution methods offer a flexible toolkit for the analysis of univariate differences; relative density clouds bring some of the same advantages to fruition in the context of multivariate research. They can assist in the exploration of complex patterns of group differences, and help break them down into simpler, more interpretable effects. An easy-to-use R function is provided to make this visualization method widely accessible to researchers.

SUBMITTER: Del Giudice M

PROVIDER: S-EPMC10298761 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Relative density clouds: Visualizing and exploring multivariate patterns of group differences.

Del Giudice Marco M

PloS one 20230627 6

This paper introduces relative density clouds, a simple but powerful method to visualize the relative density of two groups in multivariate space. Relative density clouds employ k-nearest neighbor density estimates to provide information about group differences throughout the entire distribution of the variables. The method can also be used to decompose overall group differences into the specific contributions of differences in location, scale, and covariation. Existing relative distribution met ...[more]

PMID: 37368918

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Project description:BackgroundCancer genomes are peppered with somatic mutations imprinted by different mutational processes. The mutational pattern of a cancer genome can be used to identify and understand the etiology of the underlying mutational processes. A plethora of prior research has focused on examining mutational signatures and mutational patterns from single base substitutions and their immediate sequencing context. We recently demonstrated that further classification of small mutational events (including substitutions, insertions, deletions, and doublet substitutions) can be used to provide a deeper understanding of the mutational processes that have molded a cancer genome. However, there has been no standard tool that allows fast, accurate, and comprehensive classification for all types of small mutational events.ResultsHere, we present SigProfilerMatrixGenerator, a computational tool designed for optimized exploration and visualization of mutational patterns for all types of small mutational events. SigProfilerMatrixGenerator is written in Python with an R wrapper package provided for users that prefer working in an R environment. SigProfilerMatrixGenerator produces fourteen distinct matrices by considering transcriptional strand bias of individual events and by incorporating distinct classifications for single base substitutions, doublet base substitutions, and small insertions and deletions. While the tool provides a comprehensive classification of mutations, SigProfilerMatrixGenerator is also faster and more memory efficient than existing tools that generate only a single matrix.ConclusionsSigProfilerMatrixGenerator provides a standardized method for classifying small mutational events that is both efficient and scalable to large datasets. In addition to extending the classification of single base substitutions, the tool is the first to provide support for classifying doublet base substitutions and small insertions and deletions. SigProfilerMatrixGenerator is freely available at https://github.com/AlexandrovLab/SigProfilerMatrixGenerator with an extensive documentation at https://osf.io/s93d5/wiki/home/ .

Dataset Information

Relative density clouds: Visualizing and exploring multivariate patterns of group differences.

Publications

Relative density clouds: Visualizing and exploring multivariate patterns of group differences.

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