From 06446eb635b862221f9b217c9a1b96875bad5cba Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Tue, 11 Jun 2024 12:50:03 -0400
Subject: [PATCH 1/3] chore: cleanup

---
 R/image_registration.R | 29 -----------------------------
 1 file changed, 29 deletions(-)

diff --git a/R/image_registration.R b/R/image_registration.R
index ec973892a..cdd120cdc 100644
--- a/R/image_registration.R
+++ b/R/image_registration.R
@@ -1018,32 +1018,3 @@ registerImagesFIJI <- function(
     return(0 == system(cmd))
 }
 
-
-
-
-
-
-
-# TODO - merge jython function into normal register FIJI
-# TODO - add in manual rigid registration when given a transforms table
-
-### Under Construction ####
-
-# resizeImagesFIJI = function(fiji = fiji()) {}
-
-# TODO - install FIJI jython registration and resize scripts
-# install_FIJI_scripts = function(fiji = fiji()) {}
-
-# TODO These things require a correct set of boundary values
-# - Subset images in Giotto using Magick and followup reassignment as the
-# default 'image'
-# - Follow this up with potential registration
-# - Need a way to determine the pixel distances between spots to get an idea of
-# which regions of image 'belong' to a spot
-# - Would be nice to be able to put together an image mask even in magick and
-# apply it to the image to aid with img_reg and take care of jagged lines after
-# image subsetting
-# - A shiny app to subset tissue regions would be nice
-# The shiny app should be able to select spots in a 2d plane by default
-# If given the ability, it should also select spots of a single plane or within
-# a certain range of z values and plot them as a 2D for selection purposes

From cf8232c0bd7619d04bbe24e3cda8a16aa5772614 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Wed, 3 Jul 2024 14:41:05 -0400
Subject: [PATCH 2/3] chore: remove ggrepel dep

- rely on re-exported function from GiottoVisuals
---
 DESCRIPTION          | 3 +--
 R/auxiliary_giotto.R | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a8426d509..fd2f54709 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -40,9 +40,8 @@ Imports:
     data.table (>= 1.12.2),
     dbscan (>= 1.1-3),
     ggplot2 (>= 3.1.1),
-    ggrepel,
     GiottoUtils (>= 0.1.9),
-    GiottoVisuals (>= 0.2.2),
+    GiottoVisuals (>= 0.2.4),
     igraph (>= 1.2.4.1),
     jsonlite,
     limma,
diff --git a/R/auxiliary_giotto.R b/R/auxiliary_giotto.R
index 11dafbe7a..82a65fd15 100644
--- a/R/auxiliary_giotto.R
+++ b/R/auxiliary_giotto.R
@@ -437,7 +437,7 @@ filterCombinations <- function(
     pl <- pl + scale_color_discrete(
         guide = guide_legend(title = "threshold(s)")
     )
-    pl <- pl + ggrepel::geom_text_repel(data = result_DT, aes(
+    pl <- pl + geom_text_repel(data = result_DT, aes(
         x = removed_cells + x_axis_offset,
         y = removed_feats + y_axis_offset,
         label = combination

From 348974bbc5da4413f11603f4c7d73699cda81937 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Wed, 10 Jul 2024 11:07:27 -0400
Subject: [PATCH 3/3] fix: incorrect gstat formula generation

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

diff --git a/R/kriging.R b/R/kriging.R
index ff3da4505..70ab6f585 100644
--- a/R/kriging.R
+++ b/R/kriging.R
@@ -194,7 +194,7 @@ setMethod(
                     # model to use
                     model <- gstat::gstat(
                         id = feat,
-                        formula = as.formula(paste(feat, "~ 1")),
+                        formula = as.formula(sprintf("`%s` ~ 1"), feat),
                         locations = ~ sdimx + sdimy,
                         data = annotatedlocs,
                         nmax = 7,