volcano3d - v2.0.9

• Update URLs in README.md and vignette
• Update author and maintainer email addresses
• Add @return documentation to calc_pvals, calc_stats_2x3, and significance_subset functions

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Published by KatrionaGoldmann about 3 years ago

volcano3d - v2.0.8

• Add back fc_cutoff option
• 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
• Add example of piping radial_plotly to webGL for increased speed
• Fix labels and pass through of arguments in radial_plotly

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Published by myles-lewis over 3 years ago

volcano3d - v2.0.0

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
• volcanoplot and volcanotrio functions have been deprecated and removed
• Bug fixes

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Published by myles-lewis almost 4 years ago

volcano3d - Add camera scene

• Add argument for scene camera in volcano3D

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Published by KatrionaGoldmann about 5 years ago

volcano3d - CRAN v1.1.0

• 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
• fix legend dropping levels in volcano_trio
• update volcano3D xy limits to prevent titles disappearing
• allow flexible colour-coding in standard volcano plot
• add offset for 3D axis titles
• Allow changes to the hover text

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Published by KatrionaGoldmann over 5 years ago