3D Volcano Plots and Polar Plots for Three-Class Data
Add mode bar button to rotate the plot
Boxplot to compare groups
Calculate one-way test and pairwise tests
Calculate p-values for 2x3-way analysis
2 x 3 factor DESeq2 analysis
Convert 2x3 design DESeq2 objects to a volcano3d object
Convert DESeq2 objects to a volcano3d object
Forest plot individual gene from 2x3 factor analysis
An S4 class to define the polar grid coordinates system.
Coordinates for Three Way Polar Plot
Coordinates for three way polar plot from 2x3 factor analysis
Grid required for 3D volcano plot and 2D radial plots
'Ggplot' for Three Way Polar Plot
Three-way radial comparison Polar Plot (using plotly)
Plots grid objects for inspection using plotly
Extract a subset population
PEAC synovial sample data
PEAC synovial gene expression data
An S4 class to define the polar coordinates.
Three-Dimensional Volcano Plot
Convert RNA-Seq count data to a volcano3d object using 'limma voom'
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.
Useful links