getSignatures: fail when not specifiying tax.level with exact.tax.lev…

…el=FALSE
waldronlab · Oct 14, 2024 · b973847 · b973847
1 parent 5b35f87
commit b973847
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: bugsigdbr
-Version: 1.11.2
+Version: 1.11.3
 Title: R-side access to published microbial signatures from BugSigDB
 Authors@R: c(
     person(given = "Ludwig",

diff --git a/R/getSignatures.R b/R/getSignatures.R
@@ -30,7 +30,8 @@ getSignatures <- function(df,
                           tax.id.type = c("ncbi", "metaphlan", "taxname"),
                           tax.level = "mixed",
                           exact.tax.level = TRUE,
-                          min.size = 1) {
+                          min.size = 1)
+{
     stopifnot(is.data.frame(df))
     tax.id.type <- match.arg(tax.id.type)
 
@@ -41,6 +42,11 @@ getSignatures <- function(df,
              paste(TAX.LEVELS, collapse = ", "),
              " }")
 
+    is.spec.tax.level <- length(tax.level) == 1 && tax.level != "mixed" 
+    if(!exact.tax.level && !is.spec.tax.level)
+        stop("Using exact.tax.level = FALSE requires ",
+             "to select a specific taxonomic level")
+
     # rm NA signatures
     nna <- !is.na(df[["MetaPhlAn taxon names"]])
     df <- df[nna,]