Merge pull request #981 from jiajic/patch_interpolatefeatures

fix: `interpolateFeatures()` formula generation

DESCRIPTION

@@ -40,7 +40,6 @@ Imports:
     data.table (>= 1.12.2),
     dbscan (>= 1.1-3),
     ggplot2 (>= 3.1.1),
-    ggrepel,
     GiottoUtils (>= 0.1.9),
     GiottoVisuals (>= 0.2.4),
     igraph (>= 1.2.4.1),

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

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

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,