From 930dc58e566c0a95f4414d822c7fe973b60e25fd Mon Sep 17 00:00:00 2001
From: Kasper Skytte Andersen <github@kasper.slmail.me>
Date: Fri, 17 May 2024 12:14:53 +0200
Subject: [PATCH] forgot to document new params

---
 R/amp_load.R      | 5 ++++-
 man/amp_load.Rd   | 8 +++++++-
 man/findOTUcol.Rd | 4 +++-
 3 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/R/amp_load.R b/R/amp_load.R
index 08dcb63..9dd0485 100644
--- a/R/amp_load.R
+++ b/R/amp_load.R
@@ -63,6 +63,7 @@ parseTaxonomy <- function(x) {
 #' @title Detect OTU/ASV column in a data frame
 #'
 #' @param x A data frame
+#' @param OTUcolname Character vector with columns names to search for OTUs/ASVs
 #'
 #' @return A data frame
 #' @keywords internal
@@ -269,7 +270,9 @@ import <- function(x, ...) {
 #' @param fasta (\emph{optional}) Path to a FASTA file with reference sequences for all OTU's in the OTU-table. (\emph{default:} \code{NULL})
 #' @param tree (\emph{optional}) Path to a phylogenetic tree file which will be read using \code{\link[ape]{read.tree}}, or an object of class \code{"phylo"}. (\emph{default:} \code{NULL})
 #' @param pruneSingletons (\emph{logical}) Remove OTU's only observed once in all samples. (\emph{default:} \code{FALSE})
-#' @param removeAbsentOTUs (\emph{logical}) Remove OTU's with 0 abundance in all samples. Absent OTUs are rarely in the input data itself, but can occur when some samples are removed because of a mismatch between samples in the OTU-table and sample metadata. (\emph{default:} \code{TRUE})
+#' @param removeAbsentOTUs (\emph{logical}) Remove OTU's with 0 abundance in all samples. Absent OTUs are rarely present in the input data itself, but can occur when some samples are removed because of a mismatch between samples in the OTU-table and sample metadata. (\emph{default:} \code{TRUE})
+#' @param otutable_OTUcolname Character vector with the name(s) of the column in the otutable that contains the OTUs/ASVs.
+#' @param taxonomy_OTUcolname Character vector with the name(s) of the column in the taxonomy that contains the OTUs/ASVs.
 #' @param ... (\emph{optional}) Additional arguments are passed on to any of the file reader functions used.
 #'
 #' @return A list of class \code{"ampvis2"} with 3 to 5 elements.
diff --git a/man/amp_load.Rd b/man/amp_load.Rd
index bbf25e1..32f9112 100644
--- a/man/amp_load.Rd
+++ b/man/amp_load.Rd
@@ -12,6 +12,8 @@ amp_load(
   tree = NULL,
   pruneSingletons = FALSE,
   removeAbsentOTUs = TRUE,
+  otutable_OTUcolname = c("OTU", "ASV", "#OTU ID"),
+  taxonomy_OTUcolname = c("OTU", "ASV", "#OTU ID"),
   ...
 )
 }
@@ -28,7 +30,11 @@ amp_load(
 
 \item{pruneSingletons}{(\emph{logical}) Remove OTU's only observed once in all samples. (\emph{default:} \code{FALSE})}
 
-\item{removeAbsentOTUs}{(\emph{logical}) Remove OTU's with 0 abundance in all samples. Absent OTUs are rarely in the input data itself, but can occur when some samples are removed because of a mismatch between samples in the OTU-table and sample metadata. (\emph{default:} \code{TRUE})}
+\item{removeAbsentOTUs}{(\emph{logical}) Remove OTU's with 0 abundance in all samples. Absent OTUs are rarely present in the input data itself, but can occur when some samples are removed because of a mismatch between samples in the OTU-table and sample metadata. (\emph{default:} \code{TRUE})}
+
+\item{otutable_OTUcolname}{Character vector with the name(s) of the column in the otutable that contains the OTUs/ASVs.}
+
+\item{taxonomy_OTUcolname}{Character vector with the name(s) of the column in the taxonomy that contains the OTUs/ASVs.}
 
 \item{...}{(\emph{optional}) Additional arguments are passed on to any of the file reader functions used.}
 }
diff --git a/man/findOTUcol.Rd b/man/findOTUcol.Rd
index 0f75a4e..408f569 100644
--- a/man/findOTUcol.Rd
+++ b/man/findOTUcol.Rd
@@ -4,10 +4,12 @@
 \alias{findOTUcol}
 \title{Detect OTU/ASV column in a data frame}
 \usage{
-findOTUcol(x)
+findOTUcol(x, OTUcolname = c("OTU", "ASV", "#OTU ID"))
 }
 \arguments{
 \item{x}{A data frame}
+
+\item{OTUcolname}{Character vector with columns names to search for OTUs/ASVs}
 }
 \value{
 A data frame