v2.0.0.9000

myTAI 2.0.0

Major Changes

New S7 Class System

• Migrated from traditional R data structures to modern S7 classes
• New PhyloExpressionSet S7 class replaces the old data.frame-based format
• New TestResult S7 class for standardized storage of statistical test results
• Computed properties automatically calculate derived values like TXI, pTXI, conditions, etc.
• Built-in data validation and type checking through S7 properties
• Improved replicate data handling with automatic collapsing

Function Name Modernization

Function names have been updated to use snake_case convention:

Statistical Tests (old → new)

• FlatLineTest() → flatline_test()
• ReductiveHourglassTest() → reductive_hourglass_test()
• EarlyConservationTest() → early_conservation_test()
• LateConservationTest() → late_conservation_test()
• ReverseHourglassTest() → reverse_hourglass_test()
• PairwiseTest() → pairwise_test()

Visualization Functions (old → new)

• PlotSignature() → plot_signature()
• PlotPattern() → plot_signature()
• PlotContribution() → plot_contribution()
• PlotDistribution() → plot_distribution_strata()
• PlotCategoryExpr() → plot_strata_expression()
• PlotRE() → plot_relative_expression_line()
• PlotBarRE() → plot_relative_expression_bar()
• PlotGeneSet() → plot_gene_profiles()
• PlotMeans, PlotVars, PlotMedians → plot_strata_expression(aggregate_FUN="mean"/"var"/"median")
• PlotSignatureMultiple() → plot_signature_multiple()
• PlotSignatureTransformed() → plot_signature_transformed()
• PlotSignatureGeneQuantiles() → plot_signature_gene_quantiles()

Utility Functions (old → new)

• TAI() → Computed property of PhyloExpressionSet (still accessible via TAI())
• TDI() → Computed property of PhyloExpressionSet (still accessible via TDI())
• TEI() → Computed property of PhyloExpressionSet (still accessible via TEI())
• TPI() → Computed property of PhyloExpressionSet (still accessible via TPI())
• pTAI(), pTDI → sTXI() (generalized for all transcriptomic indices)
• pMatrix() → pTXI()
• CollapseReplicates() → collapse, Built into PhyloExpressionSet constructor
• Expressed() → lowly_expressed_genes()
• MatchMap() → match_map()
• SelectGeneSet() → select_genes()
• TopExpressionGenes() → top_expression_genes()
• TopVarianceGenes() → top_variance_genes()
• REMatrix() → rel_exp_matrix()
• RE() → relative_expression()
• omitMatrix() → omit_matrix()
• is.ExpressionSet() → Built into S7 validation
• age.apply() → age.apply() (unchanged)
• tf() → tf() or transform_counts()
• tfPS() → tfPS() (unchanged)
• tfStability() → tf_stability()
• taxid() → taxid() (unchanged)

New Functions

• destroy_pattern(): Apply GATAI algorithm to identify pattern-contributing genes
• plot_signature_multiple(): Plot multiple signatures on the same plot
• plot_signature_gene_quantiles(): Plot signature with gene expression quantiles
• plot_signature_transformed(): Plot signatures with different transformations
• plot_sample_space(): Visualize sample relationships using PCA or UMAP
• plot_mean_var(): Mean-variance relationship plots
• plot_gene_profiles(): Individual gene expression profiles
• plot_distribution_expression(): Expression distribution plots
• plot_distribution_pTAI(): Partial TXI distribution plots
• plot_distribution_pTAI_qqplot(): Q-Q plots for pTXI distributions
• plot_distribution_strata(): Phylostrata distribution plots
• plot_gene_heatmap(): Gene expression heatmaps
• plot_gene_space(): Gene space visualization
• plot_cullen_frey(): Cullen-Frey plots for distribution assessment
• plot_null_txi_sample(): Null TXI sample plots
• as_PhyloExpressionSet(): Convert data to PhyloExpressionSet S7 object
• get_sc_TAI(): Single-cell TAI computation for Seurat objects
• diagnose_test_robustness(): Diagnose statistical test robustness
• remove_genes(): Remove genes from PhyloExpressionSet
• PS_colours(): Generate phylostratum color palettes
• ConservationTestResult(): S7 class for conservation test results
• TestResult(): S7 class for statistical test results

Enhanced Features

• Improved performance with parallelized C++ functions using RcppArmadillo
• All plots now use ggplot2 with consistent styling
• Comprehensive unit tests
• Updated to use modern R packages (ggplot2, dplyr, etc.)

Breaking Changes

• Function names have been updated to snake_case convention
• PhyloExpressionSet is now an S7 object instead of a data.frame
• Function signatures have been updated for consistency
• Some deprecated functions have been removed
• New package dependencies: S7, RcppArmadillo

Migration Guide

To migrate from myTAI 1.x to 2.0:

1. Convert data format:

   # Old format (data.frame)
   old_phyex <- PhyloExpressionSetExample
   
   # New format (S7 object)
   new_phyex <- as_PhyloExpressionSet(old_phyex)

2. Update function calls:

   # Old syntax
   PlotSignature(phyex_set, TestStatistic = "FlatLineTest")
   
   # New syntax
   plot_signature(phyex_set, conservation_test = flatline_test)

3. Access computed properties:

   # Old syntax
   tai_values <- TAI(phyex_set)
   
   # New syntax
   tai_values <- phyex_set@TXI
   # or
   tai_values <- TAI(phyex_set)