NEWS

myTAI 2.3.1

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)

myTAI 2.2.0.9006

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 2.0.0.9000

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)

myTAI 1.0.2.9000

New Functions

• New function tfPS() : Perform transformation of phylostratum values, analogous to PS() which transforms expression levels. Currently, tfPS() supports quantile rank transformation.
• New function PairwiseTest() : Statistically evaluate the pairwise difference in the phylotranscriptomic pattern between two contrasts based on or computations.
• New function pairScore() : Compute pairwise difference in TAI (or TDI) score.

Bug and Issue Fixes

• Removed taxonomy() and references to it due to the deprecation of taxize(). This is needed for CRAN submission.

myTAI 1.0.1.9000

New Functions

• New function PlotSignatureTransformed() : Plot evolutionary signatures across transcriptomes and RNA-seq transformations

• New function tfStability(): Perform Permutation Tests Under Different Transformations (to test the robustness of the p-values of a given test (e.g. FlatLineTest(), ReductiveHourglassTest(), ReverseHourglassTest(), EarlyConservationTest() and LateConservationTest()) to expression data transformations)

• New function LateConservationTest() : Perform Reductive Late Conservation Test (to test for a high-mid-low (or high-high-low) TAI or TDI pattern)

• New function lcScore() : Compute the Hourglass Score for the LateConservationTest

• internal rcpp functions are now using Eigen to automatically enable parallelization

New Features

• PlotSignature() updated to be able to perform the TestStatistic = "LateConservationTest".

• PlotSignature() now prints p-value as a subtitle rather than via ggplot2::annotate().

• tf() now has a pseudocount parameter, which is useful for performing logarithmic transformations when there are genes with 0 counts.

• tf() now supports vst and rlog transformations from DESeq2.

• tf() now has an intergerise parameter, which is needed when applying vst or rlog transformations.

• tf() updated documentation for performing rank transformation, which assigns ranks to the gene expression values within each stage, based on their relative positions compared to other values.

• Improvements to existing test functions (ecScore(), rhScore() and reversehourglassScore()) to give a message when the phylotranscriptomic pattern is unlikely to follow the test statistics.

• FlatLineTest() - newly returns the ks test statistics for the fitting of gamma

• FlatLineTest() - improved fitting

• FlatLineTest() - cpp functions are newly parallelized and progress bar is implemented for the computation of permutations

Bug and Issue Fixes

• Some changes to remove errors and warnings from devtools::test() and devtools::check(), when building this package, which has been accumulated from previous updates.

myTAI 1.0.0

New Functions

• New function TEI(): Compute the Transcriptome Evolutionary Index
• New function pMatrixTEI: Compute Partial Transcriptome Evolutionary Index (TEI) Values
• New function pStrataTEI: Compute Partial Transcriptome Evolutionary Index (TEI) Strata Values
• New function bootTEI: Compute a Permutation Matrix of Transcriptome Evolutionary Index (TEI)
• new internal rcpp functions to support parallel C++ computations for TEI(), pMatrixTEI(), pStrataTEI(), bootTEI()

New Features

• CollapseReplicates() now returns tibble objects
• PlotCategoryExpr() received a new argument y.ticks

Bug and Issue Fixes

• CollapseFromTo() now has an exception when a replicate number 1 is passed to the function -> previously this would cause an error to occur

myTAI 0.9.3

• removing the depreciated std::random_shuffle() function to sample plylostratum or divergence stratum columns and replacing it with std::shuffle(). See full discussion here.
• removing depreciated function calls such as dplyr::funs() and tibble::is.tibble()
• updated unit tests

myTAI 0.9.2

• changing maintainer email-address

myTAI 0.9.1

• fixing a unit test that uses set.seed(123) which causes an error in the new R version 3.6.0 due to the switch from a non-uniform "Rounding" sampler to a "Rejection" sampler in the new R version; the corresponding unit test test-PlotEnrichment.R was adjusted accordingly. Here the CRAN statement:

Note that this ensures using the (old) non-uniform “Rounding” sampler for all 3.x versions of R, and does not add an R version dependency. Note also that the new “Rejection” sampler which R will use from 3.6.0 onwards by default is definitely preferable over the old one, so that the above should really only be used as a temporary measure for reproduction of the previous behavior (and the run time tests relying on it).

myTAI 0.9.0

New Functions

• new function ReverseHourglassTest() to perform a Reverse Hourglass Test. The Reverse Hourglass Test aims to statistically evaluate the existence of a reverse hourglass pattern based on TAI or TDI computations. The corresponding p-value quantifies the probability that a given TAI or TDI pattern (or any phylotranscriptomics pattern) does follow an hourglass like shape. A p-value < 0.05 indicates that the corresponding phylotranscriptomics pattern does rather follow a reverse hourglass (low-high-low) shape.

• new function reversehourglassScore() for computing the Reverse Hourglass Score for the Reverse Hourglass Test

Updated Functionality

• function PlotSignature() receives a new TestStatistic (TestStatistic = "ReverseHourglassTest") to perform a revserse hourglass test (= testing the significance of a low-high-low pattern)

myTAI 0.8.0

Updated Functionality

• fix remaining issues when input is a tibble

myTAI 0.7.0

Updates

New Functions

• new function PlotCIRatio() to compute and visualize TAI/TDI etc patters using bootstrapping and confidence intervals (contributed by @ljljolinq1010)

Update Functionality

• all functions can now handle tibble data as input -> before there were errors thrown when input data wasn’t in strict data.frame format

myTAI 0.6.0

Updates

• is.ExpressionSet() now prints out more detailed error messages when ExpressionSet is violated

• adapt PlotContribution() to new version of dplyr where summarise_each() is deprecated.

Error message occurring after new dplyr release was:

2. Failure: PlotContribution() works properly with DivergenceExpressionSet input… (@test-PlotContribution.R#16) PlotContribution(DivergenceExpressionSetExample, legendName = “DS”) produced messages.

summarise_each() is deprecated. Use summarise_all(), summarise_at() or summarise_if() instead. To map funs over all variables, use summarise_all() summarise_each() is deprecated. Use summarise_all(), summarise_at() or summarise_if() instead. To map funs over all variables, use summarise_all()

Is now fixed.

myTAI 0.5.0

New Functions

• new function PlotSignature() allows users to plot evolutionary signatures across transcriptomes (based on ggplot2 -> new main visualization function aiming to replace the PlotPattern() function)

• new function TPI() allows users to compute the Transcriptome Polymorphism Index introduced by Gossmann et al., 2015.

• new function PlotMedians() allows users to compute and visualize the median expression of all age categories

• new function PlotVars() allows users to compute and visualize the expression variance of all age categories

Updates

• PlotContribution() is now based on ggplot2 and loses base graphics arguments

• now R/RcppExports.R and src/rcpp_funcs.cpp are included in the package due to previous compilation problems (see also stackoverflow discussion)

• MatchMap() is now based on dplyr::inner_join() to match age category table with a gene expression dataset

• PlotCorrelation() has been extended and optimized for producing high publication quality plots

• PlotMeans() is now based on ggplot2 and lost all base graphics arguments.

• PlotRE() is now based on ggplot2 and lost all base graphics arguments.

Vignettes

• In Introduction vignette: complete restructuring of the Introduction
• In Introduction vignette: add new ggplot2 based examples

myTAI 0.4.0

New Functions

• a new function PlotSelectedAgeDistr() allowing unsers to visualize the PS or DS gene distribution of a subset of genes stored in the input ExpressionSet object
• a new function PlotGroupDiffs() allowing users to plot the significant differences between gene expression distributions of PS or DS groups
• a new function GroupDiffs() allowing users to perform statistical tests to quantify the gene expression level differences between all genes of defined PS or DS groups

Updates

• PlotDistribution() now uses ggplot2 to visualize the PS or DS distribution and is also based on the new function PlotSelectedAgeDistr(); furthermore it loses arguments plotText and ... and gains a new argument legendName

• remove arguments ‘main.text’ and ‘…’ from PlotCorrelation()

• PlotCorrelation() is now based on ggplot2

• PlotGroupDiffs() receives a new argument gene.set allowing users to statistically quantify the group specific PS/DS differences of a selected set of genes

• analogously to PlotGroupDiffs() the function GroupDiffs() also receives a new argument gene.set allowing users to statistically quantify the group specific PS/DS differences of a selected set of genes

• Fixing wrong x-axis labeling in PlotCategoryExpr() when type = "stage-centered" is specified

• PlotCategoryExpr() now also prints out the PS/DS absolute frequency distribution of the selected gene.set

myTAI 0.3.0

Vignettes

• adding examples for PlotCategoryExpr() to Advanced Vignette
• adding examples for PlotReplicateQuality() to Expression vignette

New Functions

• a new function PlotCategoryExpr() allowing users to plot the expression levels of each age or divergence category as boxplot, dot plot or violin plot
• a new function PlotReplicateQuality() allowing users to visualize the quality of biological replicates

myTAI 0.2.1

Vignettes

• fixed a wrong example in the Enrichment vignette (https://github.com/HajkD/myTAI/commit/8d52fd60c274361dc9028dec3409abf60a738d8a)

Updates

• PlotGeneSet() and SelectGeneSet() now have a new argument use.only.map specifying whether or not instead of using a standard ExpressionSet a Phylostratigraphic Map or Divergene Map is passed to the function.
• a wrong version of the edgeR Bioconductor package was imported causing version 0.2.0 to fail R CMD Check on unix based systems

myTAI 0.2.0

Vignettes

• adding new vignette Taxonomy providing spep by step instructions on retrieving taxonomic information for any organism of interest

• adding new vignette Expression Analysis providing use cases to perform gene expression data analysis with myTAI

• adding new vignette Enrichment providing step-by-step instructions on how to perform PS and DS enrichment analyses with PlotEnrichment()

• adding examples for pStrata(), pMatrix(), pTAI(), pTDI(), and PlotContribution() to the Introduction Vignette

New Functions

• a new function taxonomy() allows users to retrieve taxonomic information for any organism of interest; this function has been taken from the biomartr package and was removed from biomartr afterwards. Please notice, that in myTAI version 0.1.0 the Introduction vignette referenced to the taxonomy() function in biomartr. This is no longer the case (since myTAI version 0.2.0), because now taxonomy() is implemented in myTAI.

• the new taxonomy() function is based on the powerful R package taxize.

• a new function SelectGeneSet() allows users to fastly select a subset of genes in an ExpressionSet

• a new function DiffGenes() allows users to perform differential gene expression analysis with ExpressionSet objects

• a new function EnrichmentTest() allows users to perform a Fisher’s exact test based enrichment analysis of over or underrepresented Phylostrata or Divergence Strata within a given gene set without having to plot the result

• a new function PlotGeneSet() allows users to visualize the expression profiles of a given gene set

• a new function PlotEnrichment() allows users to visualize the Phylostratum or Divergence Stratum enrichment of a given Gene Set as well as computing Fisher’s exact test to quantify the statistical significance of enrichment

• a new function PlotContribution() allows users to visualize the Phylostratum or Divergence Stratum contribution to the global TAI/TDI pattern

• a new function pTAI() allows users to compute the phylostratum contribution to the global TAI pattern

• a new function pTDI() allows users to compute the divergence stratum contribution to the global TDI pattern

Updates

• FilterRNASeqCT() has been renamed to Expressed() allowing users to apply this filter function to RNA-Seq data as well as to microarray data
• PlotRE() and PlotMeans() are now based on colors from the RColorBrewer package (default)
• PlotRE() and PlotMeans() now have a new argument colors allowing unsers to choose custom colors for the visualized relative or mean expression profiles
• geom.mean() and harm.mean() now are external functions accessible to the myTAI user

myTAI 0.1.0

Main News

• now all functions have unit tests

New Functions

• a new function pStrata() allows users to compute partial TAI/TDI values for all Phylostrata or Divergence Strata

• a new function CollapseReplicates() allows users to combine replicate expression levels in ExpressionSet objects

• a new function FilterRNASeqCT() allows users to filter expression levels of ExpressionSet objects deriving from RNA-Seq count tables

Updates

• function MatchMap() now receives a new argument remove.duplicates allowing users to delete duplicate gene ids (that might be stored in the input PhyoMap or DivergenceMap) during the process of matching a Map with an ExpressionSet

• FlatLineTest(), ReductiveHourglassTest(), EarlyConservationTest(), and PlotPattern() implement a new argument custom.perm.matrix allowing users to pass their own (custom) permutation matrix to the corresponding function. All subsequent test statistics and p-value/std.dev computations are then based on this custom permutation matrix

• EarlyConservationTest() and ReductiveHourglassTest() now have a new parameter gof.warning allowing users to choose whether or not non significant goodness of fit results should be printed as warning

• now when specifying TestStatistic = NULL in PlotPattern() only the TAI/TDI profile is drawn (without performing any test statistics); this is equavalent to performing: plot(TAI(PhyloExpressionSetExample)

• function combinatorialSignificance() is now named CombinatorialSignificance()

• changing the title and description of the myTAI package

• some minor changes in vignettes and within the documentation of functions

myTAI 0.0.2

New Features in v. 0.0.2

• combinatorialSignificance(), FlatLineTest(), ReductiveHourglassTest(), and EarlyConservationTest() now support multicore processing

• MatchMap() has been entirely rewritten and is now based on dplyr; additionally it now has a new argument accumulate that allows you to accumulate multiple expression levels to a unique expressiion level for a unique gene id

Vignettes

All three Vignettes: Introduction, Intermediate, and Advanced have been updated and extended.

Bug Fixes

• two small bugs in ReductiveHourglassTest() and EarlyConservationTest() have been fixed that caused that instead of displaying 3 or 4 plots (par(mfrow=c(1,3)) or par(mfrow=c(2,2))) only 1 plot has been generated

• a small bug in PlotMeans() that caused the visualization of a wrong y-axis label when plotting only one group of Phylostrata or Divergence Strata

myTAI 0.0.1

Introducing myTAI 0.0.1:

A framework to perform phylotranscriptomics analyses for Evolutionary Developmental Biology research.