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Handle one, zero, or unrecognized extra columns in tabulate_allele_names #83

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Merged
ressy merged 3 commits into from
May 11, 2022
Merged

Handle one, zero, or unrecognized extra columns in tabulate_allele_names #83

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637091e
Merge branch 'fix-80-row-ordering' into release-0.4.0
ressy May 11, 2022
7aeae4f
For #82: failing tests for tabulate_allele_names
ressy May 11, 2022
5827c1e
For #82: handle more extra_cols cases
ressy May 11, 2022
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12 changes: 10 additions & 2 deletions R/report.R
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,14 @@ normalize_alleles <- function(data) {
#'
#' @export
tabulate_allele_names <- function(data, extra_cols=NULL) {
if (length(extra_cols)) {
badcols <- extra_cols[! extra_cols %in% colnames(data)]
if (length(badcols)) {
stop(
paste("undefined extra columns in tabulate_allele_names: ",
badcols, collapse = " "))
}
}
# Order and replicate (for homozygous) the allele names
nms <- normalize_alleles(data[, c("Allele1Name", "Allele2Name")])
# Create unique (aside from Locus) identifiers for each entry
Expand Down Expand Up @@ -69,8 +77,8 @@ tabulate_allele_names <- function(data, extra_cols=NULL) {
sep = "_")
colnames(tbl) <- c("ID", extra_cols, allele_cols)
# If extra columns were given, re-order output rows using those
if (! is.null(extra_cols)) {
tbl <- tbl[order_entries(tbl[, extra_cols]), ]
if (length(extra_cols)) {
tbl <- tbl[order_entries(tbl[, extra_cols, drop = FALSE]), ]
}
tbl
}
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19 changes: 17 additions & 2 deletions tests/testthat/test_report.R
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Expand Up @@ -95,10 +95,25 @@ with(test_data, {
Replicate = integer(3) * NA,
stringsAsFactors = FALSE)
with(results_summary_data, {
# The basic case: sample and replicate columns
tbl <- tabulate_allele_names(results$summary,
extra_cols = c("Sample", "Replicate"))
tbl <- tbl[, 1:3]
expect_equivalent(tbl, tbl_known)
expect_true(all(c("Sample", "Replicate") %in% colnames(tbl)))
expect_equivalent(tbl[, 1:3], tbl_known)
# What about just one column name? (We'd better be using drop=FALSE!)
tbl <- tabulate_allele_names(results$summary,
extra_cols = "Sample")
expect_true("Sample" %in% colnames(tbl))
expect_false("Replicate" %in% colnames(tbl))
expect_equivalent(tbl[, 1:2], tbl_known[, 1:2])
# Unknown column name
expect_error({
tabulate_allele_names(results$summary,
extra_cols = "DoesNotExist")
}, "undefined extra columns")
# Empty column name vector -> same as not given
tbl <- tabulate_allele_names(results$summary, extra_cols = character())
expect_true(all(! c("Sample", "Replicate") %in% colnames(tbl)))
})
})

Expand Down