Build a small example VISTA object — example

Creates a lightweight VISTA object from built-in package datasets (count_data and sample_metadata) for use in examples and tutorials. The default call returns a precomputed object to keep examples and package checks fast. Non-default argument combinations fall back to rebuilding the object from the packaged example inputs.

Usage

example_vista(n_genes = 150, n_per_group = 3, method = "deseq2")

Arguments

n_genes: Number of genes to include (default 150).
n_per_group: Number of samples per group (control and treatment1) to include (default 3).
method: Differential expression backend passed to create_vista().

Value

A VISTA object.

Examples

v <- example_vista()
v
#> class: VISTA 
#> dim: 123 6 
#> metadata(12): de_results de_summary ... design comparison
#> assays(2): norm_counts counts
#> rownames(123): ENSG00000000003 ENSG00000000419 ... ENSG00000006607
#>   ENSG00000006625
#> rowData names(1): baseMean
#> colnames(6): SRR1039508 SRR1039512 ... SRR1039513 SRR1039517
#> colData names(14): SampleName cell ... sizeFactor sample_names
#> -------- VISTA --------
#> group column: cond_long (control, treatment1)
#> comparisons: treatment1_VS_control
#> DE source: deseq2
#> cutoffs: |log2FC| >= 1, padj <= 0.05
#> raw counts: available via counts()
#> schema: 1.1.0