Learn R Programming

volcano3D (version 2.0.9)

3D Volcano Plots and Polar Plots for Three-Class Data

Description

Generates interactive plots for analysing and visualising three-class high dimensional data. It is particularly suited to visualising differences in continuous attributes such as gene/protein/biomarker expression levels between three groups. Differential gene/biomarker expression analysis between two classes is typically shown as a volcano plot. However, with three groups this type of visualisation is particularly difficult to interpret. This package generates 3D volcano plots and 3-way polar plots for easier interpretation of three-class data.

Copy Link

Version

Install

install.packages('volcano3D')

Monthly Downloads

229

Version

2.0.9

License

GPL-2

Issues

Pull Requests

Stars

Forks

Maintainer

Katriona Goldmann

Last Published

May 17th, 2023

Functions in volcano3D (2.0.9)

add_animation

Add mode bar button to rotate the plot
deseq_2x3

2 x 3 factor DESeq2 analysis
calc_pvals

Calculate one-way test and pairwise tests
polar_coords

Coordinates for Three Way Polar Plot
calc_stats_2x3

Calculate p-values for 2x3-way analysis
volc3d-class

An S4 class to define the polar coordinates.
deseq_polar

Convert DESeq2 objects to a volcano3d object
polar_coords_2x3

Coordinates for three way polar plot from 2x3 factor analysis
volcano3D

Three-Dimensional Volcano Plot
forest_plot

Forest plot individual gene from 2x3 factor analysis
polar_grid

Grid required for 3D volcano plot and 2D radial plots
deseq_2x3_polar

Convert 2x3 design DESeq2 objects to a volcano3d object
show_grid

Plots grid objects for inspection using plotly
boxplot_trio

Boxplot to compare groups
syn_example_meta

PEAC synovial sample data
syn_example_rld

PEAC synovial gene expression data
significance_subset

Extract a subset population
voom_polar

Convert RNA-Seq count data to a volcano3d object using 'limma voom'
radial_ggplot

'Ggplot' for Three Way Polar Plot
radial_plotly

Three-way radial comparison Polar Plot (using plotly)
grid-class

An S4 class to define the polar grid coordinates system.