Plot Signature Under Different Transformations

Compare transcriptomic signatures under various data transformations to assess the robustness of phylotranscriptomic patterns.

Usage

plot_signature_transformed(phyex_set, transformations = COUNT_TRANSFORMS, ...)

Arguments

phyex_set

A PhyloExpressionSet object (BulkPhyloExpressionSet or ScPhyloExpressionSet)

transformations

Named list of transformation functions (default: COUNT_TRANSFORMS)

...

Additional arguments passed to plot_signature_multiple

Value

A ggplot2 object showing signatures under different transformations

Details

This function applies different transformations to the same dataset and compares the resulting transcriptomic signatures. This is useful for assessing whether phylotranscriptomic patterns are robust to different data processing approaches or are artifacts of specific transformations.

The analysis works with both bulk and single-cell data, helping to determine whether phylotranscriptomic patterns are consistent across different normalization and transformation methods.

Examples

# Compare signatures under all default transformations for bulk data
# p <- plot_signature_transformed(bulk_phyex_set)

# Single-cell data with custom transformations
# custom_transforms <- list(raw = identity, log = log1p)
# p2 <- plot_signature_transformed(sc_phyex_set, transformations = custom_transforms)