Create a plot of the transcriptomic index signature across developmental stages or cell types, with options for showing individual samples/cells and statistical testing.
plot_signature(
phyex_set,
show_reps = TRUE,
show_p_val = TRUE,
conservation_test = stat_flatline_test,
colour = NULL,
...
)A ggplot2 object showing the transcriptomic signature
A PhyloExpressionSet object (BulkPhyloExpressionSet or ScPhyloExpressionSet)
Logical, whether to show individual replicates
Logical, whether to show conservation test p-value
Function, conservation test to use for p-value calculation
Character, custom color for the plot elements
Additional arguments passed to specific methods
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)
# Basic signature plot for bulk data
p <- plot_signature(example_phyex_set)
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