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Plot Transcriptomic Signature

Source: R/plot_signature.R
plot_signature.Rd

Create a plot of the transcriptomic index signature across developmental stages or cell types, with options for showing individual samples/cells and statistical testing.

Usage

plot_signature(
  phyex_set,
  show_reps = TRUE,
  show_p_val = TRUE,
  conservation_test = stat_flatline_test,
  colour = NULL,
  ...
)

Arguments

phyex_set

A PhyloExpressionSet object (BulkPhyloExpressionSet or ScPhyloExpressionSet)

show_reps

Logical, whether to show individual replicates

show_p_val

Logical, whether to show conservation test p-value

conservation_test

Function, conservation test to use for p-value calculation

colour

Character, custom color for the plot elements

...

Additional arguments passed to specific methods

Value

A ggplot2 object showing the transcriptomic signature

Details

This function creates visualizations appropriate for the data type:

**Bulk data (BulkPhyloExpressionSet):** - Line plots showing TXI trends across developmental stages - Optional individual biological replicates as jittered points - Optional conservation test p-values

**Single-cell data (ScPhyloExpressionSet):** - Sina plots showing TXI distributions across cell types or other identities - Mean TXI values overlaid as line - Optional individual cells using geom_sina for better visualization - Flexible identity selection from metadata via additional parameters: - `primary_identity`: Character, name of metadata column for x-axis (default: current selected identities) - `secondary_identity`: Character, name of metadata column for coloring/faceting - `facet_by_secondary`: Logical, whether to facet by secondary identity (default: FALSE uses colouring)

Examples

# Basic signature plot for bulk data
# p1 <- plot_signature(bulk_phyex_set)

# Bulk plot with replicates and p-value
# p2 <- plot_signature(bulk_phyex_set, show_reps = TRUE, show_p_val = TRUE)

# Single-cell plot with individual cells
# p3 <- plot_signature(sc_phyex_set, show_reps = TRUE)

# Single-cell plot with custom primary identity
# p4 <- plot_signature(sc_phyex_set, primary_identity = "day")

# Single-cell plot with primary and secondary identities (colored)
# p5 <- plot_signature(sc_phyex_set, primary_identity = "day", secondary_identity = "condition")

# Single-cell plot with faceting by secondary identity
# p6 <- plot_signature(sc_phyex_set, primary_identity = "day", 
#                      secondary_identity = "condition", facet_by_secondary = TRUE)