From f41142b2ec009462b45302e2919e62a3d8849033 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Wed, 16 Oct 2024 09:46:42 -0400
Subject: [PATCH 01/28] temp

---
 R/clustering.R       | 30 +++++++++++++++++-------------
 man/labelTransfer.Rd |  9 +++++----
 2 files changed, 22 insertions(+), 17 deletions(-)

diff --git a/R/clustering.R b/R/clustering.R
index f57dd4f84..7ca8141e8 100644
--- a/R/clustering.R
+++ b/R/clustering.R
@@ -3321,19 +3321,23 @@ setGeneric("labelTransfer",
 
 #' @rdname labelTransfer
 #' @export
-setMethod("labelTransfer", signature(x = "giotto", y = "giotto"), function(x, y,
-    spat_unit = NULL,
-    feat_type = NULL,
-    labels,
-    k = 10,
-    name = paste0("trnsfr_", labels),
-    prob = TRUE,
-    reduction = "cells",
-    reduction_method = "pca",
-    reduction_name = "pca",
-    dimensions_to_use = 1:10,
-    return_gobject = TRUE,
-    ...) {
+setMethod("labelTransfer", signature(x = "giotto", y = "giotto"), function(
+        x, y,
+        spat_unit = NULL,
+        feat_type = NULL,
+        labels,
+        k = 10,
+        name = paste0("trnsfr_", labels),
+        prob = TRUE,
+        co_filter_params = list(),
+        co_norm_params = list(),
+
+        reduction_name = NULL,
+        reduction_method = NULL,
+        dimensions_to_use = NULL,
+        return_gobject = TRUE,
+        ...
+) {
     # NSE vars
     temp_name <- cell_ID <- temp_name_prob <- NULL
 
diff --git a/man/labelTransfer.Rd b/man/labelTransfer.Rd
index dbf876a0b..230768609 100644
--- a/man/labelTransfer.Rd
+++ b/man/labelTransfer.Rd
@@ -16,10 +16,11 @@ voting}
   k = 10,
   name = paste0("trnsfr_", labels),
   prob = TRUE,
-  reduction = "cells",
-  reduction_method = "pca",
-  reduction_name = "pca",
-  dimensions_to_use = 1:10,
+  co_filter_params = list(),
+  co_norm_params = list(),
+  reduction_name = NULL,
+  reduction_method = NULL,
+  dimensions_to_use = NULL,
   return_gobject = TRUE,
   ...
 )

From 3436f4934a090d6dcbe3031195769947f8576df0 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Wed, 30 Oct 2024 17:24:29 -0400
Subject: [PATCH 02/28] chore: bump version for dev and drop remotes

---
 DESCRIPTION | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 2f88d432a..37810e3f1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 4.1.4
+Version: 4.1.5
 Authors@R: c(
 	person("Ruben", "Dries", email = "rubendries@gmail.com",
 		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
@@ -108,10 +108,6 @@ Suggests:
     trendsceek,
     testthat (>= 3.0.0),
     rmarkdown
-Remotes:
-    drieslab/GiottoUtils,
-    drieslab/GiottoClass,
-    drieslab/GiottoVisuals
 Collate:
     'ONTraC_wrapper.R'
     'auxiliary_giotto.R'

From 578f39ef3424daf351cb26c5908a9b5566a96406 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Wed, 6 Nov 2024 13:40:38 -0500
Subject: [PATCH 03/28] Update convenience_xenium.R

---
 R/convenience_xenium.R | 145 +++++++++++++++++++++++++++++------------
 1 file changed, 104 insertions(+), 41 deletions(-)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index fa305be0b..d7e52dfe9 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -317,6 +317,7 @@ setMethod(
         # load image call
         img_fun <- function(path,
     name = "image",
+    output_dir,
     micron = obj@micron,
     negative_y = TRUE,
     flip_vertical = FALSE,
@@ -325,6 +326,7 @@ setMethod(
             .xenium_image(
                 path = path,
                 name = name,
+                output_dir = output_dir,
                 micron = micron,
                 negative_y = negative_y,
                 flip_vertical = flip_vertical,
@@ -371,7 +373,7 @@ setMethod(
         "UnassignedCodeword",
         "NegControlCodeword"
     ),
-    load_images = NULL,
+    load_images = "focus",
     load_aligned_images = NULL,
     load_expression = FALSE,
     load_cellmeta = FALSE,
@@ -483,10 +485,28 @@ setMethod(
 
 
             # images
+            load_images <- lapply(load_images, normalizePath)
+            img_focus_path <- normalizePath(img_focus_path)
+            
+            # [exception] handle focus image dir
+            is_focus <- load_images == "focus" | load_images == img_focus_path
+            # split the focus image dir away from other entries
+            focus_dir <- load_images[is_focus][[1]]
+            load_images <- load_images[!is_focus]
+            
+            # ignore any name the focus dir has
+            focus_dir <- as.character(focus_dir)
+            names(focus_dir) <- NULL
+            
+            focus_files <- list.files(focus_dir, full.names = TRUE)
+            nbound <- length(focus_files) - 1L
+            focus_names <- c("dapi", sprintf("bound%d", seq_len(nbound)))
+            names(focus_files) <- focus_names
+            
+            # append to rest of entries
+            load_images <- c(load_images, focus_files)
+            
             if (!is.null(load_images)) {
-                # replace convenient shortnames
-                load_images[load_images == "focus"] <- img_focus_path
-
                 imglist <- list()
                 imnames <- names(load_images)
                 for (impath_i in seq_along(load_images)) {
@@ -500,7 +520,7 @@ setMethod(
             }
 
             # aligned images can be placed in random places and do not have
-            # a standardized naming scheme.
+            # a standardized naming scheme. Cannot load with expected default.
 
             if (!is.null(load_aligned_images)) {
                 aimglist <- list()
@@ -1041,9 +1061,10 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
 
 ## image ####
 
+
 .xenium_image <- function(path,
     name,
-    # output_dir,
+    output_dir,
     micron,
     negative_y = TRUE,
     flip_vertical = FALSE,
@@ -1055,37 +1076,39 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
             "No path to image file provided or auto-detected"
         ), call. = FALSE)
     }
-
-    # # [directory input] -> load as individual .ome paths with defined names
-    # # intended for usage with single channel stain focus images
-    # if (checkmate::test_directory_exists(path)) {
-    #     if (missing(output_dir)) output_dir <- file.path(path, "tif_exports")
-    #     # find actual image paths in directory
-    #     ome_paths <- list.files(path, full.names = TRUE, pattern = ".ome")
-    #     # parse ome metadata for images names
-    #     ome_xml <- ometif_metadata(
-    #         ome_paths[[1]], node = "Channel", output = "data.frame"
-    #     )
-    #     # update names with the channel names
-    #     name <- ome_xml$Name
-    #
-    #     # do conversion if file does not already exist in output_dir
-    #     vmsg(.v = verbose, "> ometif to tif conversion")
-    #     lapply(ome_paths, function(ome) {
-    #         try(silent = TRUE, { # ignore fail when already written
-    #             ometif_to_tif(
-    #                 # can pass overwrite = TRUE via ... if needed
-    #                 ome, output_dir = output_dir, ...
-    #             )
-    #         })
-    #     })
-    #     # update path param
-    #     path <- list.files(output_dir, pattern = ".tif", full.names = TRUE)
-    # }
+    
+    # *** whether .ome or not does not matter for this function *** #
 
     # set default if still missing
     if (missing(name)) name <- "image"
 
+    # [directory input] -> load as individual image paths
+    # these need to be expanded then appended to running named list of images
+    is_dir <- vapply(path, dir.exists, FUN.VALUE = logical(1L))
+    dir_path <- path[is_dir]
+    dir_name <- name[is_dir]
+    path <- path[!is_dir]
+    name <- name[!is_dir]
+    
+    # expand directory inputs
+    if (length(dir_path) > 0L) {
+        for (dir_i in seq_along(dir_path)) {
+            dp_i <- dir_path[[dir_i]] # dir path
+            dn_i <- dir_name[[dir_i]] # dir name
+            vmsg(.is_debug = TRUE, "img dir input:", dp_i)
+            
+            # expand and update to per-image
+            dfp_i <- list.files(dp_i, full.names = TRUE) # dir file paths
+            dfn_i <- sprintf("%s_%d", dn_i, seq_along(dfp_i)) # dir file names
+            vmsg(.is_debug = TRUE, "* [img paths]:\n", paste(dfp_i, collapse = "\n"))
+            vmsg(.is_debug = TRUE, "* [img names]:\n", paste(dfn_i, collapse = "\n"))
+
+            # append to single file lists
+            path <- c(path, dfp_i)
+            name <- c(name, dfn_i)
+        }
+    }
+
     # [paths]
     # check files exist
     vapply(path, checkmate::assert_file_exists, FUN.VALUE = character(1L))
@@ -1105,9 +1128,11 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
         p <- pbar(along = path)
 
         gimg_list <- lapply(seq_along(path), function(img_i) {
+            # handle .ome conversion and image subobject creation
             gimg <- .xenium_image_single(
                 path = path[[img_i]],
                 name = name[[img_i]],
+                output_dir = output_dir,
                 micron = micron,
                 negative_y = negative_y,
                 flip_vertical = flip_vertical,
@@ -1121,12 +1146,19 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
     return(gimg_list)
 }
 
+# per image...
+# if .ome : check that converted output path file exists.
+#   if exists && if overwrite : remove converted image
+#   if still not exist : create converted image
+# use image
 .xenium_image_single <- function(path,
     name = "image",
+    output_dir,
     micron,
     negative_y = TRUE,
     flip_vertical = FALSE,
     flip_horizontal = FALSE,
+    overwrite = FALSE,
     verbose = NULL) {
     vmsg(.v = verbose, sprintf("loading image as '%s'", name))
     vmsg(.v = verbose, .is_debug = TRUE, path)
@@ -1139,14 +1171,45 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
         .prefix = ""
     )
 
-    # warning to for single channel .ome.tif images that terra::rast() and
-    # gdal still have difficulties with. May be related to JP2OpenJPEG driver
-    # but even loading this does not seem to fix it.
-    if (file_extension(path) %in% "ome") {
-        warning(wrap_txt(
-            ".ome.tif images not fully supported.
-            If reading fails, try converting to a basic tif `ometif_to_tif()`"
-        ))
+    # terra::rast() and gdal still have difficulties with 10x single channel 
+    # .ome.tif images. May be related to JP2OpenJPEG driver but even loading
+    # this does not seem to fix it.
+    if ("ome" %in% file_extension(path)) {
+        if (missing(output_dir)) {
+            # default output dir is a new folder under the same directory
+            output_dir <- file.path(dirname(path), "tif_exports")
+        }
+        
+        # check for existence of converted tiff file in output dir
+        # fullpath of tiff to write
+        tiff_path <- file.path(output_dir, basename(path))
+        if (checkmate::test_file_exists(tiff_path)) {
+            vmsg(.is_debug = TRUE, sprintf(
+                "converted tiff already present\n%s", tiff_path
+            ))
+            # if found AND overwrite, remove it to be regenerated downstream
+            if (isTRUE(overwrite)) {
+                unlink(tiff_path, force = TRUE)
+            }
+            # the convenience fun can be run multiple times on the dataset
+            # So, we allow directly using already converted imgs
+        }
+        
+        # check the fullpath again
+        if (!checkmate::test_file_exists(tiff_path)) {
+            vmsg(.is_debug = TRUE, sprintf(
+                "converting ome to tif\n%s", tiff_path
+            ))
+            # if missing, do conversion
+            # output is expected at `tiff_path`
+            ometif_to_tif(
+                input_file = path,
+                output_dir = output_dir,
+                overwrite = overwrite
+            )
+        }
+    
+        path <- tiff_path
     }
 
     img <- createGiottoLargeImage(path,

From ae212be87a5f55520080189d10611f9c897cb675 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Wed, 6 Nov 2024 13:41:37 -0500
Subject: [PATCH 04/28] Revert "temp"

This reverts commit f41142b2ec009462b45302e2919e62a3d8849033.
---
 R/clustering.R       | 30 +++++++++++++-----------------
 man/labelTransfer.Rd |  9 ++++-----
 2 files changed, 17 insertions(+), 22 deletions(-)

diff --git a/R/clustering.R b/R/clustering.R
index 7ca8141e8..f57dd4f84 100644
--- a/R/clustering.R
+++ b/R/clustering.R
@@ -3321,23 +3321,19 @@ setGeneric("labelTransfer",
 
 #' @rdname labelTransfer
 #' @export
-setMethod("labelTransfer", signature(x = "giotto", y = "giotto"), function(
-        x, y,
-        spat_unit = NULL,
-        feat_type = NULL,
-        labels,
-        k = 10,
-        name = paste0("trnsfr_", labels),
-        prob = TRUE,
-        co_filter_params = list(),
-        co_norm_params = list(),
-
-        reduction_name = NULL,
-        reduction_method = NULL,
-        dimensions_to_use = NULL,
-        return_gobject = TRUE,
-        ...
-) {
+setMethod("labelTransfer", signature(x = "giotto", y = "giotto"), function(x, y,
+    spat_unit = NULL,
+    feat_type = NULL,
+    labels,
+    k = 10,
+    name = paste0("trnsfr_", labels),
+    prob = TRUE,
+    reduction = "cells",
+    reduction_method = "pca",
+    reduction_name = "pca",
+    dimensions_to_use = 1:10,
+    return_gobject = TRUE,
+    ...) {
     # NSE vars
     temp_name <- cell_ID <- temp_name_prob <- NULL
 
diff --git a/man/labelTransfer.Rd b/man/labelTransfer.Rd
index 230768609..dbf876a0b 100644
--- a/man/labelTransfer.Rd
+++ b/man/labelTransfer.Rd
@@ -16,11 +16,10 @@ voting}
   k = 10,
   name = paste0("trnsfr_", labels),
   prob = TRUE,
-  co_filter_params = list(),
-  co_norm_params = list(),
-  reduction_name = NULL,
-  reduction_method = NULL,
-  dimensions_to_use = NULL,
+  reduction = "cells",
+  reduction_method = "pca",
+  reduction_name = "pca",
+  dimensions_to_use = 1:10,
   return_gobject = TRUE,
   ...
 )

From f61dcfd1e1589eaf9a0a8a383a5e3a05babb3df6 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Wed, 6 Nov 2024 13:57:33 -0500
Subject: [PATCH 05/28] Update convenience_xenium.R

---
 R/convenience_xenium.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index d7e52dfe9..c0d084621 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -1014,6 +1014,7 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
     fname <- "rna"
     if (length(names(ex_list)) > 1L) fname <- names(ex_list)
     fname[fname == "Gene Expression"] <- "rna"
+    fname <- gsub(" ", "_", fname) # replace " " with "_" characters
 
     # lapply to process more than one if present
     eo_list <- lapply(seq_along(ex_list), function(ex_i) {

From 8b0950f6be5aea2b486634eb25a747bc5502b708 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Wed, 6 Nov 2024 14:15:19 -0500
Subject: [PATCH 06/28] temporarily lower R ver

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4c3a03d74..9ed33d372 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -26,7 +26,7 @@ URL: https://drieslab.github.io/Giotto/, https://github.com/drieslab/Giotto
 BugReports: https://github.com/drieslab/Giotto/issues
 RoxygenNote: 7.3.2
 Depends:
-    R (>= 4.4.1),
+    R (>= 4.4.0),
     methods,
     GiottoClass (>= 0.4.1)
 Imports:

From ad9314f53eae2021bb018416829141ed4bba674d Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Wed, 6 Nov 2024 16:33:13 -0500
Subject: [PATCH 07/28] Update convenience_xenium.R

---
 R/convenience_xenium.R | 24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index c0d084621..065ec7b89 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -315,7 +315,7 @@ setMethod(
         obj@calls$load_expression <- expr_fun
 
         # load image call
-        img_fun <- function(path,
+        img_fun <- function(path = img_focus_path,
     name = "image",
     output_dir,
     micron = obj@micron,
@@ -1082,6 +1082,16 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
 
     # set default if still missing
     if (missing(name)) name <- "image"
+    
+    # [names]
+    if (length(name) != length(path) &&
+        length(name) != 1) {
+        stop("length of `name` should be same as length of `path`")
+    }
+    if (length(name) == 1 &&
+        length(path) > 1) {
+        name <- sprintf("%s_%d", name, seq_along(path))
+    }
 
     # [directory input] -> load as individual image paths
     # these need to be expanded then appended to running named list of images
@@ -1109,19 +1119,11 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
             name <- c(name, dfn_i)
         }
     }
-
+    
     # [paths]
     # check files exist
     vapply(path, checkmate::assert_file_exists, FUN.VALUE = character(1L))
-    # names
-    if (length(name) != length(path) &&
-        length(name) != 1) {
-        stop("length of `name` should be same as length of `path`")
-    }
-    if (length(name) == 1 &&
-        length(path) > 1) {
-        name <- sprintf("%s_%d", name, seq_along(path))
-    }
+
     # micron
     checkmate::assert_numeric(micron)
 

From f9818351145cdc5baa41662ed362de1d6aa52f72 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Wed, 6 Nov 2024 16:43:38 -0500
Subject: [PATCH 08/28] Update convenience_xenium.R

---
 R/convenience_xenium.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index 065ec7b89..cdc8eaea9 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -1110,6 +1110,8 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
             
             # expand and update to per-image
             dfp_i <- list.files(dp_i, full.names = TRUE) # dir file paths
+            dfp_i <- dfp_i[!dir.exists(dfp_i)] # ignore dir matches 
+            # (such as the export directory)
             dfn_i <- sprintf("%s_%d", dn_i, seq_along(dfp_i)) # dir file names
             vmsg(.is_debug = TRUE, "* [img paths]:\n", paste(dfp_i, collapse = "\n"))
             vmsg(.is_debug = TRUE, "* [img names]:\n", paste(dfn_i, collapse = "\n"))

From eff1c71c8aa58000df61b32b90584ad0788ae4d9 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Wed, 6 Nov 2024 17:09:42 -0500
Subject: [PATCH 09/28] Update convenience_xenium.R

---
 R/convenience_xenium.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index cdc8eaea9..0fc37ac20 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -1065,7 +1065,7 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
 
 .xenium_image <- function(path,
     name,
-    output_dir,
+    output_dir = "default", # new tif_exports folder one layer down
     micron,
     negative_y = TRUE,
     flip_vertical = FALSE,
@@ -1180,7 +1180,7 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
     # .ome.tif images. May be related to JP2OpenJPEG driver but even loading
     # this does not seem to fix it.
     if ("ome" %in% file_extension(path)) {
-        if (missing(output_dir)) {
+        if (output_dir == "default") {
             # default output dir is a new folder under the same directory
             output_dir <- file.path(dirname(path), "tif_exports")
         }

From 8bf5431fd570a542c39ec01ccfeddbdc3057733a Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Wed, 6 Nov 2024 17:17:48 -0500
Subject: [PATCH 10/28] Update convenience_xenium.R

---
 R/convenience_xenium.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index 0fc37ac20..5c8d0a50b 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -1065,7 +1065,7 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
 
 .xenium_image <- function(path,
     name,
-    output_dir = "default", # new tif_exports folder one layer down
+    output_dir,
     micron,
     negative_y = TRUE,
     flip_vertical = FALSE,
@@ -1082,6 +1082,8 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
 
     # set default if still missing
     if (missing(name)) name <- "image"
+    # default = new tif_exports folder one layer down
+    if (missing(output_dir)) output_dir <- "default"
     
     # [names]
     if (length(name) != length(path) &&

From 0157ba8c54083addc5c253acf652b6c430d230c7 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Thu, 7 Nov 2024 08:30:47 -0500
Subject: [PATCH 11/28] fix tif path checking

---
 R/convenience_xenium.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index 5c8d0a50b..57994a66e 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -1190,6 +1190,7 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
         # check for existence of converted tiff file in output dir
         # fullpath of tiff to write
         tiff_path <- file.path(output_dir, basename(path))
+        tiff_path <- gsub(".ome.tif", ".tif", tiff_path)
         if (checkmate::test_file_exists(tiff_path)) {
             vmsg(.is_debug = TRUE, sprintf(
                 "converted tiff already present\n%s", tiff_path

From 2eb20b56ea77baa1de626c84f6cf2ee7288f91fb Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Thu, 7 Nov 2024 09:19:24 -0500
Subject: [PATCH 12/28] Update convenience_xenium.R

---
 R/convenience_xenium.R | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index 57994a66e..570edbf63 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -1013,8 +1013,19 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
     # set correct feature name
     fname <- "rna"
     if (length(names(ex_list)) > 1L) fname <- names(ex_list)
+    
+    # specific feat type naming updates
     fname[fname == "Gene Expression"] <- "rna"
-    fname <- gsub(" ", "_", fname) # replace " " with "_" characters
+    fname[fname == "Negative Control Codeword"] <- "NegControlCodeword"
+    fname[fname == "Negative Control Probe"] <- "NegControlProbe"
+    fname[fname == "Blank Codeword"] <- "UnassignedCodeword" # from legacy Xenium pipeline
+    fname[fname == "Genomic Control"] <- "GenomicControl"
+    fname[fname == "Unassigned Codeword"] <- "UnassignedCodeword"
+    fname[fname == "Deprecated Codeword"] <- "DeprecatedCodeword"
+    
+    # catch for " " characters in feat type 
+    # (no major reason for doing this. spaces just make it harder to read)
+    fname <- gsub(" ", "_", fname) 
 
     # lapply to process more than one if present
     eo_list <- lapply(seq_along(ex_list), function(ex_i) {

From 57788f03f95f4929be22e3f346bb31392b0a041d Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Thu, 7 Nov 2024 09:27:50 -0500
Subject: [PATCH 13/28] fix: allow overwrite passing though ...

---
 R/convenience_xenium.R | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index 570edbf63..6c5fbd0a8 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -322,7 +322,8 @@ setMethod(
     negative_y = TRUE,
     flip_vertical = FALSE,
     flip_horizontal = FALSE,
-    verbose = NULL) {
+    verbose = NULL,
+    ...) {
             .xenium_image(
                 path = path,
                 name = name,
@@ -331,7 +332,8 @@ setMethod(
                 negative_y = negative_y,
                 flip_vertical = flip_vertical,
                 flip_horizontal = flip_horizontal,
-                verbose = verbose
+                verbose = verbose,
+                ...
             )
         }
         obj@calls$load_image <- img_fun
@@ -1156,6 +1158,7 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
                 flip_vertical = flip_vertical,
                 flip_horizontal = flip_horizontal,
                 verbose = verbose
+                ...
             )
             p()
             return(gimg)

From 8555ccf5cc88704ac216848c78bdd8c483cd50a7 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Thu, 7 Nov 2024 10:10:43 -0500
Subject: [PATCH 14/28] fix: change when image input type is checked

---
 R/convenience_xenium.R | 54 +++++++++++++++++++++---------------------
 1 file changed, 27 insertions(+), 27 deletions(-)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index 6c5fbd0a8..1a4f41188 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -384,12 +384,6 @@ setMethod(
             load_expression <- as.logical(load_expression)
             load_cellmeta <- as.logical(load_cellmeta)
 
-            if (!is.null(load_images)) {
-                checkmate::assert_list(load_images)
-                if (is.null(names(load_images))) {
-                    stop("'load_images' must be a named list of filepaths\n")
-                }
-            }
             if (!is.null(load_aligned_images)) {
                 checkmate::assert_list(load_aligned_images)
                 if (is.null(names(load_aligned_images))) {
@@ -487,28 +481,34 @@ setMethod(
 
 
             # images
-            load_images <- lapply(load_images, normalizePath)
-            img_focus_path <- normalizePath(img_focus_path)
-            
-            # [exception] handle focus image dir
-            is_focus <- load_images == "focus" | load_images == img_focus_path
-            # split the focus image dir away from other entries
-            focus_dir <- load_images[is_focus][[1]]
-            load_images <- load_images[!is_focus]
-            
-            # ignore any name the focus dir has
-            focus_dir <- as.character(focus_dir)
-            names(focus_dir) <- NULL
-            
-            focus_files <- list.files(focus_dir, full.names = TRUE)
-            nbound <- length(focus_files) - 1L
-            focus_names <- c("dapi", sprintf("bound%d", seq_len(nbound)))
-            names(focus_files) <- focus_names
-            
-            # append to rest of entries
-            load_images <- c(load_images, focus_files)
-            
             if (!is.null(load_images)) {
+                load_images <- lapply(load_images, normalizePath)
+                img_focus_path <- normalizePath(img_focus_path)
+                
+                # [exception] handle focus image dir
+                is_focus <- load_images == "focus" | load_images == img_focus_path
+                # split the focus image dir away from other entries
+                focus_dir <- load_images[is_focus][[1]]
+                load_images <- load_images[!is_focus]
+                
+                # ignore any name the focus dir has
+                focus_dir <- as.character(focus_dir)
+                names(focus_dir) <- NULL
+                
+                focus_files <- list.files(focus_dir, full.names = TRUE)
+                nbound <- length(focus_files) - 1L
+                focus_names <- c("dapi", sprintf("bound%d", seq_len(nbound)))
+                names(focus_files) <- focus_names
+                
+                # append to rest of entries
+                load_images <- c(load_images, focus_files)
+                
+                # ensure that input is list
+                checkmate::assert_list(load_images)
+                if (is.null(names(load_images))) {
+                    stop("'load_images' must be a named list of filepaths\n")
+                }
+                
                 imglist <- list()
                 imnames <- names(load_images)
                 for (impath_i in seq_along(load_images)) {

From 52abd97749d1fa3947fdcfaf13c4c52b59d154a8 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Thu, 7 Nov 2024 10:12:43 -0500
Subject: [PATCH 15/28] fix: missing comma

---
 R/convenience_xenium.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index 1a4f41188..ec5e14a69 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -1157,7 +1157,7 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
                 negative_y = negative_y,
                 flip_vertical = flip_vertical,
                 flip_horizontal = flip_horizontal,
-                verbose = verbose
+                verbose = verbose,
                 ...
             )
             p()

From 5359eb2831929459836d47648fc7b7bbdbfcb762 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Thu, 7 Nov 2024 10:32:20 -0500
Subject: [PATCH 16/28] fix: warning that the "focus" dir does not exist

---
 R/convenience_xenium.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index ec5e14a69..a42a20e85 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -483,7 +483,7 @@ setMethod(
             # images
             if (!is.null(load_images)) {
                 load_images <- lapply(load_images, normalizePath)
-                img_focus_path <- normalizePath(img_focus_path)
+                img_focus_path <- normalizePath(img_focus_path, mustWork = FALSE)
                 
                 # [exception] handle focus image dir
                 is_focus <- load_images == "focus" | load_images == img_focus_path

From 4d357502ec9820e3f0e187b89b4d7629fba26d8d Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Thu, 7 Nov 2024 10:36:26 -0500
Subject: [PATCH 17/28] fix: focus img dir assignment

---
 R/convenience_xenium.R | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index a42a20e85..46c82b214 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -488,12 +488,8 @@ setMethod(
                 # [exception] handle focus image dir
                 is_focus <- load_images == "focus" | load_images == img_focus_path
                 # split the focus image dir away from other entries
-                focus_dir <- load_images[is_focus][[1]]
                 load_images <- load_images[!is_focus]
-                
-                # ignore any name the focus dir has
-                focus_dir <- as.character(focus_dir)
-                names(focus_dir) <- NULL
+                focus_dir <- img_focus_path
                 
                 focus_files <- list.files(focus_dir, full.names = TRUE)
                 nbound <- length(focus_files) - 1L

From a23ca0e5ca48132a6bc8c2e81e027f7013a9c3f9 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Thu, 7 Nov 2024 11:25:43 -0500
Subject: [PATCH 18/28] Update convenience_xenium.R

- make transcript loading optional in create_gobject
- change featmeta loading to after possible expr matrix loading
- silence verbosity when loading TX cols
---
 R/convenience_xenium.R | 54 ++++++++++++++++++++++++++----------------
 1 file changed, 33 insertions(+), 21 deletions(-)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index 46c82b214..4bddb3975 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -377,12 +377,20 @@ setMethod(
     ),
     load_images = "focus",
     load_aligned_images = NULL,
+    load_transcripts = TRUE,
     load_expression = FALSE,
     load_cellmeta = FALSE,
     instructions = NULL,
     verbose = NULL) {
+            load_transcripts <- as.logical(load_transcripts)
             load_expression <- as.logical(load_expression)
             load_cellmeta <- as.logical(load_cellmeta)
+            
+            if (!load_transcripts && !load_expression) {
+                warning(wrap_txt(
+                    "One of either transcripts or expression info should be loaded for a fully functioning object"
+                ))
+            }
 
             if (!is.null(load_aligned_images)) {
                 checkmate::assert_list(load_aligned_images)
@@ -418,14 +426,17 @@ setMethod(
 
 
             # transcripts
-            tx_list <- funs$load_transcripts(
-                path = transcript_path,
-                feat_type = feat_type,
-                split_keyword = split_keyword,
-                verbose = verbose
-            )
-            g <- setGiotto(g, tx_list, verbose = FALSE) # lists are fine
+            if (load_transcripts) {
+                tx_list <- funs$load_transcripts(
+                    path = transcript_path,
+                    feat_type = feat_type,
+                    split_keyword = split_keyword,
+                    verbose = verbose
+                )
+                g <- setGiotto(g, tx_list, verbose = FALSE) # lists are fine
+            }
 
+            
             # polys
             if (!is.null(load_bounds)) {
                 # replace convenient shortnames
@@ -444,19 +455,8 @@ setMethod(
                 }
                 g <- setGiotto(g, blist, verbose = FALSE)
             }
-
-
-            # feat metadata
-            fx <- funs$load_featmeta(
-                path = gene_panel_json_path,
-                # ID = symbols makes sense with the subcellular feat_IDs
-                gene_ids = "symbols",
-                # no dropcols
-                verbose = verbose
-            )
-            g <- setGiotto(g, fx, verbose = FALSE)
-
-
+            
+            
             # expression
             if (load_expression) {
                 ex <- funs$load_expression(
@@ -470,6 +470,17 @@ setMethod(
             }
 
 
+            # feat metadata
+            fx <- funs$load_featmeta(
+                path = gene_panel_json_path,
+                # ID = symbols makes sense with the subcellular feat_IDs
+                gene_ids = "symbols",
+                # no dropcols
+                verbose = verbose
+            )
+            g <- setGiotto(g, fx, verbose = FALSE)
+
+
             # cell metadata
             if (load_cellmeta) {
                 cx <- funs$load_cellmeta(
@@ -680,7 +691,8 @@ importXenium <- function(xenium_dir = NULL, qv_threshold = 20) {
     gpointslist <- createGiottoPoints(
         x = tx,
         feat_type = feat_type,
-        split_keyword = split_keyword
+        split_keyword = split_keyword,
+        verbose = FALSE
     )
 
     if (inherits(gpointslist, "list")) {

From 0559c448e47967d0f9bac692379aaf238b4b4069 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Thu, 7 Nov 2024 11:44:12 -0500
Subject: [PATCH 19/28] fix: ignore subdirectories within image focus dir

---
 R/convenience_xenium.R | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index 4bddb3975..a05df423e 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -493,22 +493,25 @@ setMethod(
 
             # images
             if (!is.null(load_images)) {
-                load_images <- lapply(load_images, normalizePath)
+                load_images <- lapply(load_images, normalizePath, mustWork = FALSE)
                 img_focus_path <- normalizePath(img_focus_path, mustWork = FALSE)
                 
                 # [exception] handle focus image dir
                 is_focus <- load_images == "focus" | load_images == img_focus_path
                 # split the focus image dir away from other entries
                 load_images <- load_images[!is_focus]
-                focus_dir <- img_focus_path
                 
-                focus_files <- list.files(focus_dir, full.names = TRUE)
-                nbound <- length(focus_files) - 1L
-                focus_names <- c("dapi", sprintf("bound%d", seq_len(nbound)))
-                names(focus_files) <- focus_names
-                
-                # append to rest of entries
-                load_images <- c(load_images, focus_files)
+                if (any(is_focus)) {
+                    focus_dir <- img_focus_path
+                    focus_files <- list.files(focus_dir, full.names = TRUE)
+                    focus_files <- focus_files[!dir.exists(focus_files)] # ignore matches to export dir
+                    nbound <- length(focus_files) - 1L
+                    focus_names <- c("dapi", sprintf("bound%d", seq_len(nbound)))
+                    names(focus_files) <- focus_names
+                    
+                    # append to rest of entries
+                    load_images <- c(load_images, focus_files)
+                }
                 
                 # ensure that input is list
                 checkmate::assert_list(load_images)

From 4a9da54a0b0a942cad797c6162a2fbc3b2e09aaa Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Thu, 7 Nov 2024 11:52:20 -0500
Subject: [PATCH 20/28] add centroid creation step

---
 R/convenience_xenium.R | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index a05df423e..7d237a6f4 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -551,6 +551,11 @@ setMethod(
                 }
                 g <- setGiotto(g, aimglist)
             }
+            
+            # centroids
+            g <- addSpatialCentroidLocations(
+                g, poly_info = list_spatial_info_names(g)[[1]]
+            )
 
             return(g)
         }

From 84c9cd2f46adcb4374d8312099adace5e567283b Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Thu, 7 Nov 2024 12:01:28 -0500
Subject: [PATCH 21/28] Update convenience_xenium.R

---
 R/convenience_xenium.R | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index 7d237a6f4..c7449f9a6 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -553,8 +553,11 @@ setMethod(
             }
             
             # centroids
-            g <- addSpatialCentroidLocations(
-                g, poly_info = list_spatial_info_names(g)[[1]]
+            spat_units_to_calc <- list_spatial_info_names(g)
+            g <- addSpatialCentroidLocations(g, 
+                poly_info = spat_units_to_calc,
+                provenance = as.list(spat_units_to_calc),
+                verbose = FALSE
             )
 
             return(g)

From 1e33aa1a720320f366443cda59b19fea9f62f39f Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Thu, 7 Nov 2024 12:25:20 -0500
Subject: [PATCH 22/28] enh: update conv. fun

- autoload focus images
- auto load pre-agg data + metadata
- skip tx by default
---
 R/convenience_xenium.R | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index c7449f9a6..85f662acb 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -1383,10 +1383,11 @@ createGiottoXeniumObject <- function(xenium_dir,
         "NegControlCodeword"
     ),
     qv_threshold = 20,
-    load_images = NULL,
+    load_images = "focus",
     load_aligned_images = NULL,
-    load_expression = FALSE,
-    load_cellmeta = FALSE,
+    load_transcripts = FALSE,
+    load_expression = TRUE,
+    load_cellmeta = TRUE,
     instructions = NULL,
     verbose = NULL) {
     x <- importXenium(xenium_dir)
@@ -1400,6 +1401,7 @@ createGiottoXeniumObject <- function(xenium_dir,
         split_keyword = split_keyword,
         load_images = load_images,
         load_aligned_images = load_aligned_images,
+        load_transcripts = load_transcripts,
         load_expression = load_expression,
         load_cellmeta = load_cellmeta,
         instructions = instructions,

From 4e4e2dd9b6d80f69bdc0c11037fa46110b9c5490 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Thu, 7 Nov 2024 12:30:32 -0500
Subject: [PATCH 23/28] revert default changes

---
 R/convenience_xenium.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index 85f662acb..6fb8bc4ad 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -1385,9 +1385,9 @@ createGiottoXeniumObject <- function(xenium_dir,
     qv_threshold = 20,
     load_images = "focus",
     load_aligned_images = NULL,
-    load_transcripts = FALSE,
-    load_expression = TRUE,
-    load_cellmeta = TRUE,
+    load_transcripts = TRUE,
+    load_expression = FALSE,
+    load_cellmeta = FALSE,
     instructions = NULL,
     verbose = NULL) {
     x <- importXenium(xenium_dir)

From 7f70a924f2c94d382b5f019cad253297c2c8e4e5 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Thu, 7 Nov 2024 12:40:49 -0500
Subject: [PATCH 24/28] update prints and run docs

---
 R/convenience_xenium.R          | 6 +++++-
 man/createGiottoXeniumObject.Rd | 3 ++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R
index 6fb8bc4ad..931ce3fa0 100644
--- a/R/convenience_xenium.R
+++ b/R/convenience_xenium.R
@@ -487,7 +487,8 @@ setMethod(
                     path = metadata_path,
                     verbose = verbose
                 )
-                g <- setGiotto(g, cx)
+                # verbose = FALSE to silence warning that meta is already generated
+                g <- setGiotto(g, cx, verbose = FALSE)
             }
 
 
@@ -553,12 +554,15 @@ setMethod(
             }
             
             # centroids
+            vmsg(.v = verbose, "calculating centroids")
             spat_units_to_calc <- list_spatial_info_names(g)
             g <- addSpatialCentroidLocations(g, 
                 poly_info = spat_units_to_calc,
                 provenance = as.list(spat_units_to_calc),
                 verbose = FALSE
             )
+            
+            vmsg(.v = verbose, "done")
 
             return(g)
         }
diff --git a/man/createGiottoXeniumObject.Rd b/man/createGiottoXeniumObject.Rd
index f803aece8..5f41859b8 100644
--- a/man/createGiottoXeniumObject.Rd
+++ b/man/createGiottoXeniumObject.Rd
@@ -14,8 +14,9 @@ createGiottoXeniumObject(
   feat_type = c("rna", "NegControlProbe", "UnassignedCodeword", "NegControlCodeword"),
   split_keyword = list("NegControlProbe", "UnassignedCodeword", "NegControlCodeword"),
   qv_threshold = 20,
-  load_images = NULL,
+  load_images = "focus",
   load_aligned_images = NULL,
+  load_transcripts = TRUE,
   load_expression = FALSE,
   load_cellmeta = FALSE,
   instructions = NULL,

From 34d10add36323ad36d7af3ffbc444a4cac7fbd14 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Thu, 7 Nov 2024 12:47:33 -0500
Subject: [PATCH 25/28] Revert "temporarily lower R ver"

This reverts commit 8b0950f6be5aea2b486634eb25a747bc5502b708.
---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9ed33d372..4c3a03d74 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -26,7 +26,7 @@ URL: https://drieslab.github.io/Giotto/, https://github.com/drieslab/Giotto
 BugReports: https://github.com/drieslab/Giotto/issues
 RoxygenNote: 7.3.2
 Depends:
-    R (>= 4.4.0),
+    R (>= 4.4.1),
     methods,
     GiottoClass (>= 0.4.1)
 Imports:

From fbdb139348fcb9c401935b50f7dfa77ac1d3e17a Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Thu, 7 Nov 2024 12:56:56 -0500
Subject: [PATCH 26/28] chore: update news

---
 NEWS.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 9ecdd4e72..fc9051371 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,10 @@
 
+# Giotto 4.1.5
+
+## Enhancements
+* `createGiottoXeniumObject()` auto loading for morphology focus images, image directory loading, auto centroid calculation, allow skipping transcript loading
+
+
 # Giotto 4.1.4 (2024/10/30)
 
 ## Changes

From 4613aa8ece7f3d6a66a3e5a7a463d5ea97a135da Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Fri, 8 Nov 2024 10:07:55 -0500
Subject: [PATCH 27/28] chore: update news

---
 NEWS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index fc9051371..146e88ee4 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,5 @@
 
-# Giotto 4.1.5
+# Giotto 4.1.5 (2024/11/08)
 
 ## Enhancements
 * `createGiottoXeniumObject()` auto loading for morphology focus images, image directory loading, auto centroid calculation, allow skipping transcript loading

From 89a031a9203c9275cb8406ac006fdb4a683d6a12 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Fri, 8 Nov 2024 10:09:15 -0500
Subject: [PATCH 28/28] chore: add back remotes

---
 DESCRIPTION | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4c3a03d74..fccb7569a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -108,6 +108,10 @@ Suggests:
     trendsceek,
     testthat (>= 3.0.0),
     rmarkdown
+Remotes:
+    drieslab/GiottoUtils,
+    drieslab/GiottoClass,
+    drieslab/GiottoVisuals
 Collate:
     'ONTraC_wrapper.R'
     'auxiliary_giotto.R'