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NEWS.md

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Rubrary 0.13.0

Major

  • plot_PCA_3D: uses plotly library to plot three dimensional scatter plots
  • plot_PCA_matrix: can accommodate numeric / continuous annotations

Minor

  • PCA_Quickstart: PCA matrix & 3d plotting examples for Beltran & penguin data sets

Rubrary 0.12.0

Major

  • plot_PCA_matrix

Minor

  • get_log_coding_geneexp uses filter_genes now
  • remove reshape2 dependency
  • remove survival related suggests
  • bug fixes

Rubrary 0.11.0

  • removed a LOT of old functions that weren't generalized very well so were probably not used anyways
  • added more examples to various functions (DE genes / GSEA)
  • reorganization of function reference/index

Rubrary 0.10.3

  • theme adjustments

Rubrary 0.10.2

  • Removed old DESeq functions, reorganized, and fixed various bugs

Rubrary 0.10.1

  • GSEAsquared functions bug fixes

Rubrary 0.10.0

  • GSEAsquared functions
    • run_GSEA_squared: main function, replicating glab.library::gsea_squared with keyword_plot_method == 1 setting
    • get_GSEAsq_terms: terms/keywords
    • and plot_GSEAsq_density moved to be with this set of functions
  • get_kspval signed enrichment score implementation and visualization based on franapoli/signed-ks-test
  • Various bug fixes

Rubrary 0.9.6

New

  • rwrite & rread: fast data.table based read-in and write-out functions

Improved

  • get_log_coding_geneexp improvements - can specify log base now

Rubrary 0.9.5

New

  • complete plot_DESeq_boxplot rewrite + rename to plot_DEgene_boxplot
    • finally !! able to remove gridExtra dependency

Rubrary 0.9.4

Improved

  • rename project_PCA to the more descriptive predict_PCA

Rubrary 0.9.3

New

  • rread: wrapper for data.table::fread() that can pull in rownames
  • project_PCA: long awaited massive PCA projection script incorporating varimax

Improved

  • Switch to Seurat::DiscretePalette for pals's alphabet color palette

Rubrary 0.9.2

Improved

  • plot_GSEA_barplot: sig_cutoff format by p value significance parameter

Rubrary 0.9.1

Improved

  • GSEA functions: improved name formatting for enrichment plot
  • plot_PCA: fixed subtitle for non-annotated plots (thanks Duncan :) )
  • plot_GSEA_barplot: formatting flexibility improvements

Rubrary 0.9.0

General

  • PCA improvements + associated vignettes
  • scRNA integration assessment metrics
  • GSEA barplot, GSEAsq density plot comparison, and associated helper functions

New

  • plot_GSEAsq_density: plot categorical percentile rank comparison between two GSEA squared signatures
  • plot_PCA_biplot: conventional biplot with loadings and standardized scores
  • plot_GSEA_barplot: function-ified version of horizontal barplot originally made for Jack
    • format_GSEA_name: cleans up MSigDB underscore + all caps names a bit
    • split_line: splits long text to multiple lines based on number of char or lines
  • rotate_varimax: Varimax rotation for prcomp output
  • assess_integration: run_LISI but more general, incorporating Seurat::MixingMetric + CellMixS::cms
    • run_LISI: wrapper for assess_integration specific to LISI
    • run_MixingMetric: wrapper for assess_integration specific to MixingMetric
    • run_CellMixS: wrapper for assess_integration specific to cms

Improved

  • run_PCA: fix eigenvector / loadings distinction
  • plot_volcano: rewritten terms + args to be more general and align better w/ EnhancedVolcano documentation
  • genes functions: added Mart arg to functions that try to query BioMart
    • plot_PC_genes -> plot_genes, still defaults to filtering by PC genes but technically any gene list can be passed in to filter dataframe by
  • plot_waterfall: a little smarter on where to place high/low value labels but still quite dumb
  • plot_scatter: color by group, more text options

Vignettes

  • PCA_Walkthrough: based on Lindsey Smith's PCA tutorial, a more step by step toy dataset for PCA including some of the math behind it
  • PCA_Quickstart: very basic Palmer Penguin demonstration of plotting scripts + replication of Graeber Beltran PCA
  • DE_Genes & GSEA: previous combined tutorial nows plit into two

Rubrary 0.8.0

General

  • Gene accessing, LISI
  • PCA functions improvements
  • Functional vignettes

New

  • get_PC_genes: accesses BioMart database for genes annotated as protein coding
  • filter_PC_genes: filter dataframe to specified list of genes, with possible Seurat::UpdateSymbolList powered gene symbol correcting. Technically this isn't specific to protein-coding filtering only and words with list input.
  • get_gene_desc: accesses BioMart database for gene description w/ list of genes input
    • Technically not specific to getting description fields given list of BioMart attrs
    • Should probably add a error/warning if gene names don't match, possible Seurat correction?
  • convert_genes: access BioMart database to convert gene name format
  • run_LISI: for Seurat obj, assess integration quantitatively by using LISI metric
    • outputs visualization to help interpret resulting values

Improved

  • run_PCA: additional documentation recommending standardization
  • plot_PCA: accommodation for passing in prcomp object, custom colors

Vignettes

  • PCA: changed to palmerpenguins dataset and have it actually run and output
  • DESeq_GSEA: working DESeq example with airway dataset

Rubrary 0.7.0

230329 function improvements

Rubrary 0.6.0

230323: new GSEA and Seurat DimPlot functions & improvements

  • plot_GSEA_pathway
  • plot_dim_set
  • hypergeo_coexp

Rubrary 0.5.0

230303: New scRNA hypergeometric p-value and plot function

  • genecoexp_scatter_hyper
  • phyper_df
  • pltAB
  • run_RRHO (WIP)

Rubrary 0.4.0

230203: new functions

  • plot_waterfall
  • plot_density
  • check_normal
  • calc_sumZscore
  • various fixes

Rubrary 0.3.0

New DESeq functions + extras

  • output_DESeq
  • filter_DESeq_PC
  • plot_DESeq_volcano
  • plot_scatter_compare
  • plot_screeplot
  • plot_scatter_mtx (WIP)

Rubrary 0.2.0

  • plot_distribution: Density plot with histo

Rubrary 0.1.5

  • Save option for "plot_scatter"

Rubrary 0.1.4

  • Optional KS pval for plot_waterfall_hl

Rubrary 0.1.3

  • plot_waterfall_hl label outside

Rubrary 0.1.2

  • Fixed export of plot_waterfall_hl.R to namespace

Rubrary 0.1.1

Rubrary 0.1.0

  • Added a NEWS.md file to track changes to the package.