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Coerce SummarizedExperiment to VISTA

as_vista.Rd

Convert a pre-existing SummarizedExperiment into a valid VISTA object.

Usage

as_vista(
  se,
  assay_name = "norm_counts",
  group_column,
  comparisons = list(),
  deg_summary = list(),
  cutoffs = list(),
  group_palette = "Dark 3",
  validate = TRUE
)

Arguments

se

A SummarizedExperiment object.

assay_name

Assay in se to use as norm_counts (default: "norm_counts").

group_column

Grouping column in colData(se).

comparisons

Optional named list of differential expression tables.

deg_summary

Optional named list of DEG summary tables.

cutoffs

Optional named list of threshold metadata.

group_palette

Palette name for group colors.

validate

Logical; run object validation before returning.

Value

A VISTA object.

Examples

mat <- matrix(rnorm(60), nrow = 10)
rownames(mat) <- paste0("gene", seq_len(nrow(mat)))
colnames(mat) <- paste0("sample", seq_len(ncol(mat)))
se <- SummarizedExperiment::SummarizedExperiment(
  assays = list(norm_counts = mat),
  colData = S4Vectors::DataFrame(
    cond = rep(c("A", "B"), each = 3),
    row.names = colnames(mat)
  ),
  rowData = S4Vectors::DataFrame(
    gene_id = rownames(mat),
    row.names = rownames(mat)
  )
)
v <- as_vista(se, group_column = "cond")
v
#> class: SummarizedExperiment 
#> dim: 10 6 
#> metadata(6): de_results de_summary ... provenance vista_schema_version
#> assays(1): norm_counts
#> rownames(10): gene1 gene2 ... gene9 gene10
#> rowData names(1): gene_id
#> colnames(6): sample1 sample2 ... sample5 sample6
#> colData names(2): cond sample_names