Subset a VISTA object — VISTA-subset • VISTA

Subsets the underlying SummarizedExperiment and keeps the analysis metadata consistent with the result.

Usage

# S4 method for class 'VISTA,ANY,ANY,ANY'
x[i, j, ..., drop = FALSE]

Arguments

x: A VISTA object.
i, j: Row (gene) and column (sample) subscripts.
...: Passed to the SummarizedExperiment method.
drop: Ignored, as for SummarizedExperiment.

Value

A VISTA object.

Details

Row (gene) subsetting reindexes every stored differential-expression table – the active de_results/de_summary and every entry of de_results_by_method/de_summary_by_method – to the retained genes, in the new row order. DEG summaries are recounted from the retained rows.

Column (sample) subsetting leaves the DE tables untouched, because they are analysis results rather than per-sample data; recomputing them would require re-running the model. Group and comparison colour maps are pruned to the groups that still have samples, and a warning names any comparison whose groups are no longer represented, since plots of that comparison no longer correspond to the samples in the object.

Each subset appends an entry to metadata(x)$provenance$subset_history.

Examples

v <- example_vista()

# DE tables follow the genes.
v10 <- v[seq_len(10), ]
nrow(comparisons(v10)[[1]])
#> [1] 10

# Sample subsetting prunes the group colour map.
v_ctrl <- v[, sample_info(v)$cond_long == "control"]
#> Warning: Comparison "treatment1_VS_control" is no longer represented by the retained
#> samples.
#> ℹ The stored results are kept unchanged; re-run `create_vista()` to analyse
#>   this subset.
group_colors(v_ctrl)
#>   control 
#> "#C87A8A"