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News

volcano3D 2.0.9

16/05/2022

• Update URLs in README.md and vignette
• update author and maintainer email addresses

volcano3D 2.0.8

23/09/2022

• Add back fc_cutoff option

volcano3D 2.0.7

09/09/2022

• Add deseq_2x3() function for 2x3 factor design comparisons using DESeq2
• Add deseq_2x3_polar() which takes results of 2x3 factor design DESeq2 comparisons generated by deseq_2x3 and converts results to a volc3d object ready for plotting
• Add polar_coords_2x3() for 2x3 factor analysis of any dataset to generate a volc3d object for plotting
• Add forest_plot for plotting genes from 2x3 factor comparisons

volcano3D 2.0.2

23/08/2022

• Add example of piping radial_plotly to webGL for increased speed
• Fix labels and pass through of arguments in radial_plotly

volcano3D 2.0.0

29/06/2022

• Major update including:
• Significantly simplified pipeline
• Streamlined polar_coords() function no longer requires a complex p-value table object
• Conduit functions to make it much easier to make 3d volcano plots and 3-way polar plots from gene expression analysis using ‘DESeq2’ and ‘limma voom’
• Inbuilt statistical tests for group comparison (one-way ANOVA) and pairwise comparisons with easy calculation of p-values and optional adjustment for multiple testing
• polar_coords() is thus able to accept more general data
• Back compatibility has been maintained for old ‘polar’ class objects
• volcano_plot and volcano_trio functions have been deprecated and removed
• Bug fixes

volcano3D 1.3.2

27/10/2021

• Allow users to extend volcano3D radial axes onto the z-axis
• add source for radial_plotly

volcano3D 1.3.1

20/09/2021

• Enable cases where one comparison may be a substring of another
• Allow instances with no significant features

volcano3D 1.3.0

27/03/2021

• Add volcano4D function for rotating/spinning volcano plots
• Add axis and grid width parameters (grid_width and axis_width respectively) to radial_plotly, radial_ggplot and volcano3D
• Add option (axes_from_origin) to allow axes to start from either the origin (default) or the first radial break in polar_grid.

volcano3D 1.2.0

25/02/2021

• Add argument for scene camera in volcano3D

volcano3D 1.1.0

04/02/2021

• allow colour coding to be based on pvalue or adjusted pvalue according to cutoff_criteria
• allow subsetting by significance groups with the significance_subset function

volcano3D 1.0.3

15/08/2020

• fix legend dropping levels in volcano_trio
• update volcano3D xy limits to prevent titles disappearing
• allow flexible colour-coding in standard volcano plot

volcano3D 1.0.2

03/07/2020

• add offset for 3D axis titles
• Allow changes to the hover text

volcano3D 1.0.1

26/06/2020

• update vignette for CRAN (remove WebGL)
• update default plotly parameters
• Allow optional colour coding of labels in radial plots
• remove ggplot warnings of NA in geom_path
• Allow colour of grids and axes to be changed
• Convert 3D labels to annotations

volcano3D 1.0.0

29/05/2020

• Combined create_dep and polar_coord functions so no longer backwards compatible.
• Combined the 3D and 2D functions of polar_grid
• Moved colour selection to individual plotting functions to make it more intuitive
• Made the fold change columns optional
• Allowed custom grid to be passed in
• Pass label columns as plotly keys in volcano3d and radial_plotly
• Pass label columns as plotly keys in volcano3d and radial_plotly
• Add plotly height and width parameters
• Add plotly boxplots
• Create default colours
• Improve polar_coords speed

volcano3D 0.1.0

27/04/2020

• This is the initial build of volcano3D

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.