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
