Visualization of Functional Analysis Data

Implementation of multilayered visualizations for enhanced graphical representation of functional analysis data. It combines and integrates omics data derived from expression and functional annotation enrichment analyses. Its plotting functions have been developed with an hierarchical structure in mind: starting from a general overview to identify the most enriched categories (modified bar plot, bubble plot) to a more detailed one displaying different types of relevant information for the molecules in a given set of categories (circle plot, chord plot, cluster plot, Venn diagram, heatmap).


Despite the plethora of methods available for the functional analysis of omics data, obtaining comprehensive- yet detailed understanding of the results remains challenging. GOplot takes the output of any general enrichment analysis and generates plots at different levels of detail: from a general overview to identify the most enriched categories (bar plot, bubble plot) to a more detailed view displaying different types of information for molecules in a given set of categories (circle plot, chord plot, cluster plot). The package provides a deeper insight into omics data and allows scientists to generate insightful plots with only a few lines of code to easily communicate the findings.

GOplot is available via CRAN: http://cran.r-project.org/web/packages/GOplot

  • the latest released version: install.packages("GOplot")
  • the latest development version: install_github("wencke/wencke.github.io")

For preprocessing: circle_dat(), chord_dat() and reduce_overlap()

For plotting: GOBubble(), GOBar(), GOChord(), GOCluster(), GOCircle(), GOVenn(), GOHeat()

A manual can be found on the website https://wencke.github.io/

News

  • Add function 'reduce_overlap' to reduce the number of redundant terms and improve readability of plots

  • Add parameter 'bg.col' to GOBubble() to enable panel background colour of facet plot

  • Add new plot function GOHeat()

  • Fix various bugs of draw_table()

  • Fix various bugs of GOVenn()

  • Fix bug of 'process.lable' argument in GOChord

  • Adjust draw_table() to new release of gridExtra

  • Add parameter 'limit' to chord_dat() to restrict the dimension of the binary martix

Reference manual

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install.packages("GOplot")

1.0.2 by Wencke Walter, a year ago


https://github.com/wencke/wencke.github.io


Report a bug at https://github.com/wencke/wencke.github.io/issues


Browse source code at https://github.com/cran/GOplot


Authors: Wencke Walter [aut, cre], Fatima Sanchez-Cabo [aut]


Documentation:   PDF Manual  


GPL-2 license


Depends on ggplot2, ggdendro, gridExtra, RColorBrewer

Suggests knitr, rmarkdown


See at CRAN