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Validate ggchord input data before plotting

Source: R/validate.R
validate_ggchord_data.Rd

Performs structured validation of seq_data, ribbon_data and gene_data so that problems can be found, understood and fixed before plotting. The result is a "ggchord_validation" object with a valid flag, errors (severe problems that make the plot misleading), warnings (drawable but noteworthy issues), per-category counts, a data summary, the original row numbers of every problem, and a list of automatically fixable issues.

Usage

validate_ggchord_data(
  seq_data,
  ribbon_data = NULL,
  gene_data = NULL,
  strict = FALSE,
  check_coordinates = TRUE,
  check_duplicates = TRUE,
  check_self_links = TRUE
)

Arguments

seq_data

data.frame/tibble, required. Basic sequence information (columns seq_id, length).

ribbon_data

data.frame/tibble, optional. Alignment results (columns qaccver, saccver, length, pident, qstart, qend, sstart, send).

gene_data

data.frame/tibble, optional. Gene annotation data (columns seq_id, start, end, strand, anno).

strict

Logical. When TRUE, stop with an error as soon as any severe problem is found. When FALSE (default), return the full diagnostic report without stopping.

check_coordinates

Logical, default TRUE. Whether to check that ribbon/gene coordinates stay inside [1, sequence length].

check_duplicates

Logical, default TRUE. Whether to look for fully duplicated, near-duplicated and highly overlapping records.

Logical, default TRUE. Whether to flag alignment rows where qaccver == saccver.

Value

A "ggchord_validation" object (a list) with at least:

valid

Logical: TRUE when there are no severe errors.

errors

data.frame of severe issues (table, category, row, column, message).

warnings

data.frame of non-severe issues (same columns).

summary

Per-category counts (table, category, severity, n).

data_summary

Counts of sequences/ribbons/genes, unknown IDs, out-of-range rows, etc.

invalid_rows

Named list of original row numbers per problem category.

cleanable

data.frame of fixable issues with suggested actions.

print() and summary() methods are provided.

Examples

library(ggchord)
data(seq_data_example)
data(ribbon_data_example)
data(gene_data_example)

res <- validate_ggchord_data(seq_data_example, ribbon_data_example,
                             gene_data_example)
res$valid
#> [1] TRUE
print(res)
#> ggchord data validation
#> ========================
#> Result: VALID (0 error(s), 0 warning(s))
#> Sequences: 4 | Ribbons: 31 | Genes: 20
summary(res)
#> ggchord validation summary
#> Valid: TRUE
#> Sequences: 4 | Ribbons: 31 | Genes: 20
#> No issues found.

# Introduce a problem: unknown sequence ID in the ribbons
bad <- transform(ribbon_data_example, saccver = "NOT_A_SEQUENCE")
v <- validate_ggchord_data(seq_data_example, bad)
v$invalid_rows$ribbon_unknown_id
#> NULL