Match count and metadata inputs for VISTA

match_vista_inputs() aligns standardized counts and sample metadata so they can be passed directly to create_vista(). It accepts the raw output from read_vista_counts() or a count data frame/matrix plus sample metadata.

Usage

match_vista_inputs(
  counts,
  sample_info,
  column_geneid = NULL,
  sample_column = NULL,
  reorder = TRUE,
  drop_unmatched = FALSE,
  verbose = TRUE
)

Arguments

counts

Standardized counts from read_vista_counts(), or a compatible count matrix/data frame.

sample_info

Sample metadata from read_vista_metadata() or a data frame coercible to that format.

column_geneid

Optional gene identifier column for raw tabular counts. Ignored when counts is the list output of read_vista_counts().

sample_column

Optional sample identifier column in sample_info.

reorder

Logical; if TRUE (default), reorder sample_info to match count columns.

drop_unmatched

Logical; if TRUE, keep only the intersection of count samples and metadata samples. Otherwise mismatches raise an error.

verbose

Logical; print an informational alignment summary.

Value

A list with standardized counts, aligned sample_info, column_geneid, sample_names, sample_name_map, row_data, and a small report.

Examples

data("count_data", package = "VISTA")
data("sample_metadata", package = "VISTA")

cnt <- read_vista_counts(
  count_data[seq_len(25), ],
  format = "matrix",
  gene_id_column = "gene_id",
  verbose = FALSE
)
si <- read_vista_metadata(
  sample_metadata[sample_metadata$sample_names %in% cnt$sample_names, ],
  verbose = FALSE
)
matched <- match_vista_inputs(cnt, si, verbose = FALSE)

matched$column_geneid
#> [1] "gene_id"
identical(matched$sample_info$sample_names, colnames(matched$counts)[-1])
#> [1] TRUE