NEWS.md

In KatrionaGoldmann/volcano3D: 3D Volcano Plots and Polar Plots for Three-Class Data

News

volcano3D 2.0.11

25/08/2023

• Fix wrong colours in plotly label annotations

volcano3D 2.0.10

14/06/2023

• 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
• 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

KatrionaGoldmann/volcano3D documentation built on Aug. 28, 2023, 7:39 a.m.