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NEWS.md

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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