GOsummaries (version 2.6.0)

GOsummaries-package: Word cloud summaries of GO enrichment analysis

Description

A package to visualize Gene Ontology (GO) enrichment analysis results on gene lists arising from different analyses such clustering or PCA. The significant GO categories are visualised as word clouds that can be combined with different plots summarizing the underlying data.

Details

The goal of GOsummaries package is to draw figures that can be used in presentations and articles. To draw them, the user should first construct a gosummaries object and then use its plot function on it. One can start constructing the gosummaries object from gene lists, with filling in all the necessary information step by step. However, there are some convenience functions for different classes of common analysis results. See gosummaries.kmeans, gosummaries.MArrayLM and gosummaries.prcomp corresponding to k-means, limma and PCA results.

The plot.gosummaries describes how to customize the plots.

The word cloud drawing function plotWordcloud in this package is implemented largely based on the code from package wordcloud, but with slight tweaks: it uses grid graphics, has some additional layout options, has more intelligent options to scale the text sizes to fit the picture and, finally, should be a bit faster since larger part of the algorithm was implemeted in C++.