first try at fixing similarity to seq

R/similiarity_to_reference.R

@@ -2,12 +2,14 @@
 #'
 #' This function takes in a set of sequences and parses a similarity matrix to extract the similarity to a reference sequence. The resulting data is filtered to return only the similarity values for the reference sequence. The function supports parallel processing with multiple cores.
 #'
-#' @param seqs A DNAStringSet object containing the sequences.
+#' @param seqs A named DNAStringSet object containing the sequences to compare to ref.
+#' @param ref A named DNAStringSet object containing the reference sequences.
 #' @param ncores An integer specifying the number of cores to use for parallel processing. Defaults to 1.
 #'
 #' @import dplyr tibble tidyr
 #' @export
-similiarity_to_reference <- function (seqs = DNAStringSet,
+similiarity_to_reference <- function (seqs = named_DNAStringSet,
+                                      ref = named_DNAStringSet,
                                       ncores = 1) {
   if(length(seqs) > 1){
     out <- alignment_based_distance_matrix(seqs = seqs,
@@ -15,7 +17,7 @@ similiarity_to_reference <- function (seqs = DNAStringSet,
       as_tibble(rownames = "query") %>%
       pivot_longer(cols = -query, names_to = "seqnames",
                    values_to = "sim_to_ref") %>%
-      mutate(seq_var = if_else(query == names(seqs)[1], "ref", "none")) %>%
+      mutate(seq_var = if_else(query == names(ref)[1], "ref", "none")) %>%
       filter(seq_var == "ref") %>%
       select(-seq_var, -query)
     }

man/similiarity_to_reference.Rd

@@ -4,10 +4,16 @@
 \alias{similiarity_to_reference}
 \title{Parse similarity matrix to extract similarity to reference}
 \usage{
-similiarity_to_reference(seqs = DNAStringSet, ncores = 1)
+similiarity_to_reference(
+  seqs = named_DNAStringSet,
+  ref = named_DNAStringSet,
+  ncores = 1
+)
 }
 \arguments{
-\item{seqs}{A DNAStringSet object containing the sequences.}
+\item{seqs}{A named DNAStringSet object containing the sequences to compare to ref.}
+
+\item{ref}{A named DNAStringSet object containing the reference sequences.}
 
 \item{ncores}{An integer specifying the number of cores to use for parallel processing. Defaults to 1.}
 }