more efficient cluster writing by only reading in seqtab_nochim once

R/per_cluster_abundance.R

@@ -3,22 +3,19 @@
 #' Primarily intended for use inside \code{\link{read_and_write_cluster_abundance}}.
 #'
 #' @param seqs_of_one_cluster DNAStringSet containing sequences of one cluster
-#' @param seqtab_nochim Path to the seqtab_nochim file (in RDS format)
+#' @param seqtab_nochim seqtab object, as imported by readRDS ("path/to/seqtab_nochim.rds")
 #' @param reference_seqs Named vector of reference sequences to exclude (Optional) or NULL (default)
 #' @return A table with the abundance of sequences within the cluster
 #' @import dplyr readr tibble tidyr
 #' @export
 
 per_cluster_abundance <- function(seqs_of_one_cluster = DNAStringSet,
-                                  seqtab_nochim = 'seqtab_nochim.rds',
+                                  seqtab_nochim = stab,
                                   reference_seqs = NULL){
-  stab <- readRDS(seqtab_nochim) %>%
-    t() %>% as.data.frame() %>%
-    rownames_to_column(var = 'seqs')
 
   seq_tbl <- tibble(seqs = as.data.frame(seqs_of_one_cluster)[[1]],
                     ID = names(seqs_of_one_cluster))
-  named_stab <- left_join(seq_tbl, stab, by = 'seqs')
+  named_stab <- left_join(seq_tbl, seqtab_nochim, by = 'seqs')
 
   if(!is.null(reference_seqs)){
     named_stab <- named_stab %>%

R/read_and_write_cluster_abundance.R

@@ -22,25 +22,10 @@ read_and_write_cluster_abundance <- function(
     seqtab_nochim = 'seqtab_nochim.rds',
     outpath = path) {
 
-# stab <- readRDS(seqtab_nochim) %>%
-#    t() %>% as.data.frame() %>%
-#    rownames_to_column(var = 'seqs')
+  stab <- readRDS(seqtab_nochim) %>%
+    t() %>% as.data.frame() %>%
+    rownames_to_column(var = 'seqs')
 
-#  per_cluster_abundance <- function(seqs_of_one_cluster = DNAStringSet){
-#    seq_tbl <- tibble(seqs = as.data.frame(seqs_of_one_cluster)[[1]],
-#                      ID = names(seqs_of_one_cluster))
-#    named_stab <- left_join(seq_tbl, stab, by = 'seqs')
-
-#    if(!is.null(reference_seqs)){
-#      named_stab <- named_stab %>%
-#        filter(!(ID %in% names(reference_seqs)))
-#    }
-
-#    stab_tbl <- named_stab %>%
-#      select(-seqs) %>%
-#      pivot_longer(cols = -ID, names_to = 'Sample', values_to = 'count')
-#  }
-#
   out <- lapply(cluster_sequence_list, per_cluster_abundance,
                 seqtab_nochim = seqtab_nochim, reference_seqs = reference_seqs)
 

man/per_cluster_abundance.Rd

@@ -6,14 +6,14 @@
 \usage{
 per_cluster_abundance(
   seqs_of_one_cluster = DNAStringSet,
-  seqtab_nochim = "seqtab_nochim.rds",
+  seqtab_nochim = stab,
   reference_seqs = NULL
 )
 }
 \arguments{
 \item{seqs_of_one_cluster}{DNAStringSet containing sequences of one cluster}
 
-\item{seqtab_nochim}{Path to the seqtab_nochim file (in RDS format)}
+\item{seqtab_nochim}{seqtab object, as imported by readRDS ("path/to/seqtab_nochim.rds")}
 
 \item{reference_seqs}{Named vector of reference sequences to exclude (Optional) or NULL (default)}
 }