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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()
Convert Data to BulkPhyloExpressionSet
as_ScPhyloExpressionSet()
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

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
downsample_expression()
Downsample Expression Matrix
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
load_example_phyex_set_sc()
Load Example Single-Cell PhyloExpressionSet
match_map()
Match Gene Expression Data with Phylostratum Map
match_map_sc()
Match Single-Cell Expression Data with Phylostratum Map
normalise_stage_expression()
Normalise Stage Expression Data
omit_matrix()
Compute TXI Profiles Omitting Each Gene
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
reorder_identities()
Set Identity Order for ScPhyloExpressionSet
select_genes()
Select Genes from PhyloExpressionSet
set_expression()
Gene Expression Transformation Functions
set_identities()
Set Identities for ScPhyloExpressionSet
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.

available_identities()
Get available identities
COUNT_TRANSFORMS
Count Transformation Functions
PS_colours()
Generate Phylostratum Colors
save_gatai_results_pdf()
Save GATAI Analysis Results to PDF
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