Change one-way ANOVA matrix test in calc_pvals() from
Rfast::ftests() to the more accurate and correct
matrixTests::col_oneway_welch()
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