Add tests; fix R CMD checks

DESCRIPTION

@@ -39,14 +39,15 @@ Imports:
     jsonlite,
     methods,
     patchwork,
+    rJava,
     rlang,
+    scales,
     tibble,
     tools,
     utils
 VignetteBuilder: knitr
 Suggests:
     knitr,
-    rJava,
     rmarkdown,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3

R/class_all_generics.R

@@ -375,3 +375,13 @@ setGeneric("readSamples", function(object, ...) standardGeneric("readSamples"))
 setGeneric("serverInfo", function(object, ...) standardGeneric("serverInfo"))
 
 
+## ----
+#' @importFrom GenomeInfoDb seqnames
+NULL
+
+
+## ----
+#' @importFrom GenomeInfoDb seqnames<-
+NULL
+
+

R/class_phg_metrics.R

@@ -630,9 +630,13 @@ setMethod(
 
 
 ## ----
+#' @title
+#' Return all contig IDs from metrics object
+#'
 #' @param x
 #' A \code{PHGMetrics} object
 #'
+#' @return A vector of unique contig IDs
 #' @importFrom GenomeInfoDb seqnames
 #' @export
 setMethod(
@@ -662,8 +666,10 @@ setMethod(
 
 
 ## ----
+#' @title
 #' Set Sequence Names for PHGMetrics Object
 #'
+#' @description
 #' This method replaces old IDs with new IDs in the `PHGMetrics` object.
 #' It ensures that both `metricAlign` and `metricGvcf` fields are updated
 #' with the new sequence names provided in the `value` data frame.
@@ -711,16 +717,16 @@ setMethod(
 
         # Helper function to replace IDs
         replaceIds <- function(x, slot_name, field, value) {
-            metrics <- slot(x, slot_name)
+            metrics <- methods::slot(x, slot_name)
             if (is.null(metrics) || length(metrics) == 0) return()
             len <- if (is(metrics, "data.frame")) 1 else length(metrics)
             for (i in seq_len(len)) {
                 oldIds <- as.character(metrics[[i]][[field]])
-                replacements <- setNames(value$new_id, value$old_id)
+                replacements <- stats::setNames(value$new_id, value$old_id)
                 newIds <- ifelse(oldIds %in% names(replacements), replacements[oldIds], oldIds)
                 metrics[[i]][[field]] <- newIds
             }
-            slot(x, slot_name) <<- metrics
+            methods::slot(x, slot_name) <<- metrics
         }
 
         # Replace IDs in metricAlign if it's not NULL

R/utils_metrics.R

@@ -243,7 +243,7 @@ metMessenger <- function(
 # }
 parseFormula <- function(formula) {
     # Extract the terms object from the formula
-    termsObj <- terms(formula)
+    termsObj <- stats::terms(formula)
 
     # Extract the response variables (LHS)
     lhsVars <- all.vars(formula[[2]])
@@ -261,7 +261,7 @@ parseFormula <- function(formula) {
     }
 
     # Check if keywords are used with other variables in RHS
-    if ("ALL" %in% lhsVars && length(rhsVars) > 1) {
+    if (any(keywords %in% rhsVars) && length(rhsVars) > 1) {
         rlang::abort(errorMsg)
     }
 

R/vis_plot_gvcf.R

@@ -43,7 +43,7 @@ plotGvcfFromMetrics <- function(df, formula, nRow, nCol, tag) {
         filtGvcfMap <- GVCF_MAP[GVCF_MAP$id %in% lhsVars, ]
     }
 
-    if (length(filtGvcfMap) == 0) {
+    if (nrow(filtGvcfMap) == 0) {
         rlang::abort("No valid metrics found in left-hand side of equation")
     }
 

tests/testthat/test_class_phg_metrics.R

@@ -117,6 +117,26 @@ test_that("PHGMetrics general metric ID return and update tests", {
         object = metricsIds(metTest),
         expected = c("toy_anchors_s01", "new_gvcf_id")
     )
+
+    # seqnames
+    expect_equal(
+        object = seqnames(metBase),
+        expected = c(
+            "1", "2", "3",
+            "Vu01", "Vu02", "Vu03", "Vu04", "Vu05",
+            "Vu06", "Vu07", "Vu08", "Vu09", "Vu10",
+            "Vu11", "contig_206", "contig_178"
+        )
+    )
+
+    metTest <- metBase
+    expect_error(object = seqnames(metTest) <- data.frame(old_id = "error"))
+    expect_error(object = seqnames(metTest) <- c("another", "error"))
+    seqnames(metTest) <- data.frame(
+        old_id = c("Vu01", "Vu03", "1"),
+        new_id = c("CHR_NEW_01", "CHR_NEW_03", "ALGN_CHR_01")
+    )
+    expect_true(all(c("CHR_NEW_01", "CHR_NEW_03", "ALGN_CHR_01") %in% seqnames(metTest)))
 })
 
 
@@ -315,11 +335,15 @@ test_that("PHGMetrics general gVCF plot tests", {
 
     metBase <- PHGMetrics(metricDir)
     expect_true(is(plotGvcf(metBase, metBase$toy_gvcf_metrics), "ggplot"))
+    expect_error(is(plotGvcf(metBase, c(metBase$toy_gvcf_metrics, metBase$toy_anchors_s01)), "ggplot"))
     expect_true(is(plotGvcf(metBase), "ggplot"))
     expect_true(is(plotGvcf(metBase, f = ALL ~ ALL), "ggplot"))
     expect_true(is(plotGvcf(metBase, f = ALL ~ Vu01 + Vu05), "ggplot"))
+    expect_true(is(plotGvcf(metBase, f = num_ns ~ Vu01 + Vu05), "ggplot"))
     expect_error(is(plotGvcf(metBase, f = ALL + CORE ~ ALL + Vu02), "ggplot"))
     expect_error(is(plotGvcf(metBase, f = CORE + num_ns ~ ALL + Vu02), "ggplot"))
+    expect_error(is(plotGvcf(metBase, f = num_nsss ~ ALL + Vu02), "ggplot"))
+    expect_error(is(plotGvcf(metBase, f = num_nsss ~ ALL), "ggplot"))
 
 })