From 56f92a1539fbbe4d8e773ad5ab28298f3be4e033 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Fri, 30 Aug 2024 11:17:38 -0400
Subject: [PATCH] fix: dimnames/colnames generics

---
 R/join.R                         |  1 -
 R/methods-names.R                | 28 +++++++++++++++++++++++++++-
 R/methods-rbind.R                |  2 +-
 man/dimnames.Rd                  | 12 ++++++++++++
 man/row-plus-colnames-generic.Rd |  4 ++++
 5 files changed, 44 insertions(+), 3 deletions(-)

diff --git a/R/join.R b/R/join.R
index 5dcd4674..c6e2a4d3 100644
--- a/R/join.R
+++ b/R/join.R
@@ -686,7 +686,6 @@ joinGiottoObjects <- function(gobject_list,
 
 
 
-
     ## spatial locations
     vmsg(.v = verbose, "3. spatial locations")
 
diff --git a/R/methods-names.R b/R/methods-names.R
index bbb9d7af..0cb6a215 100644
--- a/R/methods-names.R
+++ b/R/methods-names.R
@@ -1,12 +1,17 @@
 #' @include generics.R
 NULL
 
+# NOTE:
+# dimnames MUST be provided for rownames and colnames methods to be well
+# behaved
+
 #' @title Row and column names
 #' @name row-plus-colnames-generic
 #' @aliases colnames rownames
 #' @description Retrieve or set the row or column names of an object
 #' @param x object
 #' @return A character vector of row or col names
+#' @keywords internal
 #' @examples
 #' g <- GiottoData::loadSubObjectMini("exprObj")
 #'
@@ -19,6 +24,7 @@ NULL
 #' Retrieve or set the dimnames of an object
 #' @param x object
 #' @returns character
+#' @keywords internal
 #' @examples
 #' g <- GiottoData::loadSubObjectMini("exprObj")
 #'
@@ -60,7 +66,9 @@ setMethod("rownames", signature(x = "exprObj"), function(x) rownames(x[]))
 #' @export
 setMethod("rownames", signature(x = "dimObj"), function(x) rownames(x[]))
 
-
+#' @rdname row-plus-colnames-generic
+#' @export
+setMethod("rownames", signature(x = "metaData"), function(x) rownames(x[]))
 
 
 
@@ -71,3 +79,21 @@ setMethod("dimnames", signature(x = "exprObj"), function(x) dimnames(x[]))
 #' @rdname dimnames
 #' @export
 setMethod("dimnames", signature(x = "dimObj"), function(x) dimnames(x[]))
+
+#' @rdname dimnames
+#' @export
+setMethod("dimnames", signature(x = "spatLocsObj"), function(x) dimnames(x[]))
+
+#' @rdname dimnames
+#' @export
+setMethod("dimnames", signature(x = "metaData"), function(x) dimnames(x[]))
+
+#' @rdname dimnames
+#' @export
+setMethod("dimnames", signature(x = "enrData"), function(x) dimnames(x[]))
+
+#' @rdname dimnames
+#' @export
+setMethod("dimnames", signature(x = "dimObj"), function(x) dimnames(x[]))
+
+
diff --git a/R/methods-rbind.R b/R/methods-rbind.R
index a3b2c71f..dcd08031 100644
--- a/R/methods-rbind.R
+++ b/R/methods-rbind.R
@@ -33,7 +33,7 @@ setMethod(
             stop("rbind: `spatLocsObj` with the same IDs cannot be joined", 
                  call. = FALSE)
         }
-        
+
         # if one is 3d, ensure both are 3d
         x3 <- .is_3d_spatlocs(x)
         y3 <- .is_3d_spatlocs(y)
diff --git a/man/dimnames.Rd b/man/dimnames.Rd
index 0be71b51..dcad2fc1 100644
--- a/man/dimnames.Rd
+++ b/man/dimnames.Rd
@@ -4,10 +4,21 @@
 \alias{dimnames}
 \alias{dimnames,exprObj-method}
 \alias{dimnames,dimObj-method}
+\alias{dimnames,spatLocsObj-method}
+\alias{dimnames,metaData-method}
+\alias{dimnames,enrData-method}
 \title{Dimnames of an object}
 \usage{
 \S4method{dimnames}{exprObj}(x)
 
+\S4method{dimnames}{dimObj}(x)
+
+\S4method{dimnames}{spatLocsObj}(x)
+
+\S4method{dimnames}{metaData}(x)
+
+\S4method{dimnames}{enrData}(x)
+
 \S4method{dimnames}{dimObj}(x)
 }
 \arguments{
@@ -24,3 +35,4 @@ g <- GiottoData::loadSubObjectMini("exprObj")
 
 dimnames(g)
 }
+\keyword{internal}
diff --git a/man/row-plus-colnames-generic.Rd b/man/row-plus-colnames-generic.Rd
index ba9cf466..6bbd5a91 100644
--- a/man/row-plus-colnames-generic.Rd
+++ b/man/row-plus-colnames-generic.Rd
@@ -12,6 +12,7 @@
 \alias{colnames,dimObj-method}
 \alias{rownames,exprObj-method}
 \alias{rownames,dimObj-method}
+\alias{rownames,metaData-method}
 \title{Row and column names}
 \usage{
 \S4method{colnames}{exprObj}(x)
@@ -29,6 +30,8 @@
 \S4method{rownames}{exprObj}(x)
 
 \S4method{rownames}{dimObj}(x)
+
+\S4method{rownames}{metaData}(x)
 }
 \arguments{
 \item{x}{object}
@@ -44,3 +47,4 @@ g <- GiottoData::loadSubObjectMini("exprObj")
 
 colnames(g)
 }
+\keyword{internal}