Package index

Visualisation

Visualise and visually inspect evolutionary transcriptomics patterns as well as summary statistics.

plot_signature(): Plot Transcriptomic Signature

plot_signature_gene_quantiles(): Plot Signature Across Gene Expression Quantiles

plot_signature_multiple(): Plot Multiple Transcriptomic Signatures

plot_signature_transformed(): Plot Signature Under Different Transformations

plot_contribution(): Plot Phylostratum Contribution to Transcriptomic Index

plot_cullen_frey(): Plot Cullen-Frey Diagram for Distribution Assessment

plot_distribution_expression(): Comparing expression levels distributions across developmental stages

plot_distribution_pTAI(): Partial TAI Distribution Plotting Functions

plot_distribution_pTAI_qqplot(): QQ plot comparing partial TAI distributions across developmental stages against a reference stage

plot_distribution_strata(): Plot Distribution of Genes Across Phylostrata

plot_gatai_results(): Plot Comprehensive GATAI Results

plot_gene_heatmap(): Plot Gene Expression Heatmap

plot_gene_profiles(): Plot Individual Gene Expression Profiles

plot_gene_space(): Plot Gene Space Using PCA

plot_mean_var(): Plot Mean-Variance Relationship

plot_null_txi_sample(): Plot Null TXI Sample Distribution

plot_relative_expression_bar(): Plot Mean Relative Expression Levels as Barplot

plot_relative_expression_line(): Plot Relative Expression Profiles (Line Plot)

plot_sample_space(): Plot Sample Space Visualization

plot_strata_expression(): Plot Expression Levels by Phylostratum

Statistical tests

Functions for statistical testing of evolutionary transcriptomics patterns (with visualisation).

stat_early_conservation_test(): Early Conservation Test

stat_flatline_test(): Flat Line Test for Conservation Pattern

stat_generic_conservation_test(): Generic Conservation Test Framework

stat_late_conservation_test(): Late Conservation Test

stat_pairwise_test(): Pairwise Conservation Test

stat_reductive_hourglass_test(): Reductive Hourglass Test

stat_reverse_hourglass_test(): Reverse Hourglass Test

Data structures

Core S7 data classes used for evolutionary transcriptomics analysis.

BulkPhyloExpressionSet(): Bulk PhyloExpressionSet Class

ConservationTestResult(): Conservation Test Result S7 Class

PhyloExpressionSetBase(): PhyloExpressionSet Base Class

ScPhyloExpressionSet(): Single-Cell PhyloExpressionSet Class

TestResult(): Test Result S7 Class

Distribution(): Distribution S7 Class

Functions to convert between dataframe and BulkPhyloExpressionSet or ScPhyloExpressionSet.

as_BulkPhyloExpressionSet(): as_BulkPhyloExpressionSet

BulkPhyloExpressionSet_from_df(): Convert Data to BulkPhyloExpressionSet

ScPhyloExpressionSet_from_matrix(): Create Single-Cell PhyloExpressionSet from Expression Matrix

ScPhyloExpressionSet_from_seurat(): Convert Seurat Object to Single-Cell PhyloExpressionSet

as_data_frame(): Convert BulkPhyloExpressionSet to Data Frame

check_PhyloExpressionSet(): Check if object is a PhyloExpressionSet

check_BulkPhyloExpressionSet(): Check if object is a BulkPhyloExpressionSet

check_ScPhyloExpressionSet(): Check if object is a ScPhyloExpressionSet

Single-cell specific functions

Functions specifically designed for single-cell RNA-seq data analysis.

downsample_expression(): Downsample Expression Matrix by Groups

downsample(): Downsample ScPhyloExpressionSet

match_map_sc_matrix(): Match Expression Matrix with Phylostratum Map

match_map_sc_seurat(): Match Single-Cell Expression Data with Phylostratum Map (Seurat)

Taxonomic information retrieval

Functions to compute transcriptome indices.

taxid(): Retrieve taxonomy categories from NCBI Taxonomy

Transcriptomic index calculation

Compute full and partial evolutionary transcriptomics measures.

TAI(): Calculate Transcriptomic Age Index (TAI)

TDI(): Calculate Transcriptomic Divergence Index (TDI)

TEI(): Calculate Transcriptomic Evolutionary Index (TEI)

TPI(): Calculate Transcriptomic Polymorphism Index (TPI)

TXI(): Calculate Transcriptomic Index (TXI)

sTXI(): Calculate Stratum-Specific Transcriptomic Index

pTXI(): Calculate Phylostratum-Specific Transcriptomic Index

Functions to transform, normalise, and manipulate expression datasets.

age.apply(): Age Category Specific apply Function

collapse(): Collapse PhyloExpressionSet Replicates

destroy_pattern(): Destroy Phylotranscriptomic Pattern Using GATAI

diagnose_test_robustness(): Diagnose Test Robustness

distributions: Predefined Distribution Objects

exp_p(): Format P-Value for Scientific Notation

genes_lowly_expressed(): Select Lowly Expressed Genes

genes_top_expr(): Gene Expression Filtering Functions

genes_top_mean(): Select Top Mean Expressed Genes

genes_top_variance(): Select Top Variable Genes

match_map(): Match Gene Expression Data with Phylostratum Map

normalise_stage_expression(): Normalise Stage Expression Data

omit_matrix(): Compute TXI Profiles Omitting Each Gene

permute_PS(): Permute Strata in PhyloExpressionSet

quantile_rank(): Calculate Quantile Ranks

rel_exp_matrix(): Compute Relative Expression Matrix for PhyloExpressionSet

relative_expression(): Relative Expression Functions

remove_genes(): Remove Genes from PhyloExpressionSet

select_genes(): Select Genes from PhyloExpressionSet

set_expression(): Gene Expression Transformation Functions

strata_enrichment(): Calculate Phylostratum Enrichment

transform_counts(): Transform Expression Counts in PhyloExpressionSet

tf(): Short Alias for Transform Counts

tf_PS(): Transform Phylostratum Values

tf_stability(): Perform Permutation Tests Under Different Transformations

Utilities/Metadata

Helper functions and metadata constants.

COUNT_TRANSFORMS: Count Transformation Functions

PS_colours(): Generate Phylostratum Colors

save_gatai_results_pdf(): Save GATAI Analysis Results to PDF

gatai_animate_destruction(): Animate GATAI Destruction Process

print.TestResult: Print Method for TestResult

rename_phyex_set(): Rename a PhyloExpressionSet

TI_map: Transcriptomic Index Name Mapping

TXI_conf_int(): Confidence Intervals for Transcriptomic Index (TXI)

TXI_std_dev(): Standard Deviation for TXI

Example datasets

Example datasets for demonstrating and testing package functions.

example_phyex_set: Example phyex set

example_phyex_set_old: Example phyex set old

example_phyex_set_sc: Load Example Single-Cell PhyloExpressionSet