Skip to content
Snippets Groups Projects
Commit 8d1e165d authored by Simeon's avatar Simeon
Browse files

exporting per_cluster_abundance

was previously a purely internal function
parent 0dad8cc6
No related branches found
No related tags found
No related merge requests found
......@@ -18,6 +18,7 @@ export(find_longest_reading_frames)
export(find_repeat_positions)
export(kmer_based_distance_matrix)
export(meshclustR)
export(per_cluster_abundance)
export(pivot_cluster_tbl_wider)
export(plot_abundance_per_sample)
export(plot_abundance_sums_per_sequence)
......
#' Extract abundance of sequences from a single cluster
#'
#' 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 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',
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')
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')
}
......@@ -22,26 +22,27 @@ 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')
# 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')
}
# if(!is.null(reference_seqs)){
# named_stab <- named_stab %>%
# filter(!(ID %in% names(reference_seqs)))
# }
out <- lapply(cluster_sequence_list, per_cluster_abundance)
# 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)
write_cluster_abundance_tbl <- function(clus_name){
stab_tbl <- out[[clus_name]]
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/per_cluster_abundance.R
\name{per_cluster_abundance}
\alias{per_cluster_abundance}
\title{Extract abundance of sequences from a single cluster}
\usage{
per_cluster_abundance(
seqs_of_one_cluster = DNAStringSet,
seqtab_nochim = "seqtab_nochim.rds",
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{reference_seqs}{Named vector of reference sequences to exclude (Optional) or NULL (default)}
}
\value{
A table with the abundance of sequences within the cluster
}
\description{
Primarily intended for use inside \code{\link{read_and_write_cluster_abundance}}.
}
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment