16/05/2022
- Update URLs in README.md and vignette
- update author and maintainer email addresses
23/09/2022
- Add back
fc_cutoff option
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
23/08/2022
- Add example of piping
radial_plotly to webGL for
increased speed
- Fix labels and pass through of arguments in
radial_plotly
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
27/10/2021
- Allow users to extend volcano3D radial axes onto the z-axis
- add source for radial_plotly
20/09/2021
- Enable cases where one comparison may be a substring of another
- Allow instances with no significant features
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.
25/02/2021
- Add argument for scene camera in volcano3D
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
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
03/07/2020
- add offset for 3D axis titles
- Allow changes to the hover text
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
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
27/04/2020
- This is the initial build of volcano3D