From 36bdbdab9e0cc8181edefeba8394048103af812e Mon Sep 17 00:00:00 2001
From: Ethan Bass <ethanbass@gmail.com>
Date: Tue, 14 Nov 2023 19:27:29 -0500
Subject: [PATCH] feat: filter matches with ms_filter_alignment

---
 NEWS.md                    |  1 +
 R/read_alignment.R         | 10 +++++++---
 man/ms_filter_alignment.Rd |  5 +++--
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index f4cdf9b..1a097af 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,7 @@
 # mzinspectr 0.4.0
 
 * Changed name of package to "mzinspectr".
+* Updated `ms_filter_alignment` so it filters matches if columns are removed from the peak table.
 
 # msdialreadr 0.3.3
 
diff --git a/R/read_alignment.R b/R/read_alignment.R
index a31b961..1f3623b 100644
--- a/R/read_alignment.R
+++ b/R/read_alignment.R
@@ -30,13 +30,14 @@ ms_read_alignment <- function(path){
 
 #' Filter alignment by provided indices.
 #' @param x An \code{msdial_alignment} object or matrix with rows as samples and features as columns.
-#' @param idx Indices to be retained
-#' @param what Which dimension to filter on. Either \code{rows} or columns (\code{cols}).
+#' @param idx Indices to be retained or excluded according to the value of \code{inverse}.
+#' @param what Which dimension to filter on. Either (\code{rows}) or columns
+#' (\code{cols}).
 #' @param inverse Whether to retain (default) or remove the specified columns.
 #' @author Ethan Bass
 #' @export
 ms_filter_alignment <- function(x, idx, what=c("rows","cols"), inverse = FALSE){
-  what <- match.arg(what, c("rows","cols"))
+  what <- match.arg(what, c("rows", "cols"))
   if (inverse){
     idx <- -idx
   }
@@ -46,6 +47,9 @@ ms_filter_alignment <- function(x, idx, what=c("rows","cols"), inverse = FALSE){
   } else if (what == "cols"){
     x$tab <- x$tab[,idx]
     x$peak_meta <- x$peak_meta[idx,]
+    if (!is.null(x$matches)){
+      x$matches <- x$matches[idx]
+    }
   }
   x
 }
diff --git a/man/ms_filter_alignment.Rd b/man/ms_filter_alignment.Rd
index 2a45eff..3c7bf68 100644
--- a/man/ms_filter_alignment.Rd
+++ b/man/ms_filter_alignment.Rd
@@ -9,9 +9,10 @@ ms_filter_alignment(x, idx, what = c("rows", "cols"), inverse = FALSE)
 \arguments{
 \item{x}{An \code{msdial_alignment} object or matrix with rows as samples and features as columns.}
 
-\item{idx}{Indices to be retained}
+\item{idx}{Indices to be retained or excluded according to the value of \code{inverse}.}
 
-\item{what}{Which dimension to filter on. Either \code{rows} or columns (\code{cols}).}
+\item{what}{Which dimension to filter on. Either (\code{rows}) or columns
+(\code{cols}).}
 
 \item{inverse}{Whether to retain (default) or remove the specified columns.}
 }