diff --git a/DESCRIPTION b/DESCRIPTION index 26d84d72f..b269be49d 100644 --- a/DESCRIPTION +++ b/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), 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 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 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,