myTAI - v2.1.0.9000

myTAI 2.1.0.9000

Major Refactoring and New Features

• Single-cell support: New ScPhyloExpressionSet S7 class for single-cell data, alongside BulkPhyloExpressionSet for bulk data.
• Property renaming: conditions → identities (and conditions_label → identities_label), counts/counts_collapsed → expression/expression_collapsed.
• All core logic and plotting now robust to both bulk and single-cell objects.

Function Renaming and Prefixes

• Statistical tests: All core test functions now use the stat_ prefix:
  • flatline_test() → stat_flatline_test()
  • early_conservation_test() → stat_early_conservation_test()
  • late_conservation_test() → stat_late_conservation_test()
  • reductive_hourglass_test() → stat_reductive_hourglass_test()
  • reverse_hourglass_test() → stat_reverse_hourglass_test()
  • pairwise_test() → stat_pairwise_test()
  • generic_conservation_test() → stat_generic_conservation_test()
  • generate_conservation_txis() → stat_generate_conservation_txis()
• Gene selection/filtering: All gene selection/filtering functions now use the genes_ prefix:
  • top_expression_genes() → genes_top_mean()
  • top_variance_genes() → genes_top_variance()
  • lowly_expressed_genes() → genes_lowly_expressed()
  • filter_dyn_expr() → genes_filter_dynamic()

Other Changes

• Many internal and Rd files renamed for consistency (e.g., gene_patterns.R → genes_patterns.R, S7_utils.R → utils_S7.R).
• Deprecated/legacy files removed: expression_utils.R, single_cell.R.
• All documentation and examples updated to use new function/property names.

- R
Published by nifets 12 months ago

myTAI - 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: ```r # Old format (data.frame) old_phyex <- PhyloExpressionSetExample

# New format (S7 object) newphyex <- asPhyloExpressionSet(old_phyex) ```

1. Update function calls: ```r # Old syntax PlotSignature(phyex_set, TestStatistic = "FlatLineTest")

# New syntax plotsignature(phyexset, conservationtest = flatlinetest) ```

1. Access computed properties: ```r # Old syntax taivalues <- TAI(phyexset)

# New syntax taivalues <- phyexset@TXI # or taivalues <- TAI(phyexset) ```

- R
Published by nifets about 1 year ago

myTAI - myTAI v1.0

This is the historic version of myTAI

- R
Published by nifets about 1 year ago