The latest release of myTAI and first release of the v2 version, which is now on CRAN!

The details of this release will be added soon, in the mean time check the notes on the v2 pre-release versions!

This update has focused on improving the single-cell phyloset functionality.

The single-cell phylo expression object no longer depends on Seurat. You can construct the ScPhyloExpressionSet either from a count matrix (sparse or dense), using ScPhyloExpressionSet_from_matrix, or from a Seurat object, using ScPhyloExpressionSet_from_seurat. For consistency, one can use BulkPhyloExpressionSet_from_df instead of as_BulkPhyloExpressionSet.

One key functionality of the single-cell object is the ability to switch between different identities when plotting (equivalent to the Seurat::Idents functionality). This is done by setting the ::identities_label property of the object. The ::available_idents property can be used to see what options the user has in setting the current identity. By setting ::idents_colours[[]], the user can choose a colour pallette for the different identities when plotting, which are saved across different plotting calls.

The computation of TAI values for single cell is now cached. Moreover, we have readded the C++ accelerated code for the computation of TAI, which upon profiling shows to be faster than the R version when handling more than 100000 cells (an adaptive function chooses the appropriate implementation for the object size).

Some of the plotting functionality had been improved and more options were added for plotting (e.g. plot_gene_heatmap now allows for passing a custom colour mapping for the rows (genes), instead of colouring them by their strata; plot_signature for single cell should be more readable).

Bug fixes:

• validation of S7 objects now works properly
• printing of object information now works properly (instead of dumping all the properties information)

Most importantly, new vignettes were added and the website has been updated. Many thanks to @LotharukpongJS

Functionality wise:

• added more input validation across functions
• improved plotting in destroy_pattern
• renamed tfPS to tf_PS and fixed bug which prevented strata transformations from happening (PhyloExpressionSet now has an extra field @strata_values which keeps track of the phylostratum values)
• added back standard deviation ribbon to plot_signature
• finer control over cell identity selection in the sc object
• fixed bugs in some of the plotting functions, such as plot_signature_multiple showing the colours in reverse, plot_genes_heatmap not working when given just one gene etc.

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.

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)

This is the historic version of myTAI