Merge pull request #10157 from satijalab/revert-spatial-updates

Revert spatial updates in active development

Author: anashen

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Seurat
-Version: 5.3.1.9999
+Version: 5.3.0.9999
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
 Authors@R: c(
@@ -123,7 +123,6 @@ Suggests:
     rtracklayer,
     S4Vectors,
     sf (>= 1.0.0),
-    sp,
     SingleCellExperiment,
     SummarizedExperiment,
     testthat,

NAMESPACE

@@ -296,7 +296,6 @@ export(IntegrateData)
 export(IntegrateEmbeddings)
 export(IntegrateLayers)
 export(Intensity)
-export(InteractiveSpatialPlot)
 export(IsGlobal)
 export(JS)
 export(JackStraw)
@@ -368,10 +367,8 @@ export(RPCAIntegration)
 export(Radius)
 export(Read10X)
 export(Read10X_Coordinates)
-export(Read10X_HD_GeoJson)
 export(Read10X_Image)
 export(Read10X_ScaleFactors)
-export(Read10X_Segmentations)
 export(Read10X_h5)
 export(Read10X_probe_metadata)
 export(ReadAkoya)
@@ -726,8 +723,6 @@ importFrom(ggridges,theme_ridges)
 importFrom(grDevices,as.raster)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,colorRampPalette)
-importFrom(grDevices,dev.off)
-importFrom(grDevices,png)
 importFrom(grDevices,rgb)
 importFrom(graphics,axis)
 importFrom(graphics,image)

NEWS.md

@@ -1,8 +1,6 @@
 # Unreleased
 
 ## Changes
-
-- Added function `InteractiveSpatialPlot` to allow users to interactively lasso-select cells from a spatial Seurat object (Visium or SlideSeq data)
 - Added `label.size.cutoff` parameter to `DimPlot` to allow users to label only clusters above a certain size
 - Added option to use `cluster_leiden` from `igraph` when running Leiden clustering ([#9931](https://github.com/satijalab/seurat/pull/9931))
 - Added option to use `umap2` from `uwot` when running UMAP ([#9918](https://github.com/satijalab/seurat/pull/9918))

R/convenience.R

@@ -333,8 +333,7 @@ SpatialDimPlot <- function(
   stroke = NA,
   label.box = TRUE,
   interactive = FALSE,
-  information = NULL,
-  plot_segmentations = FALSE
+  information = NULL
 ) {
   return(SpatialPlot(
     object = object,
@@ -359,8 +358,7 @@ SpatialDimPlot <- function(
     stroke = stroke,
     label.box = label.box,
     interactive = interactive,
-    information = information,
-    plot_segmentations = plot_segmentations
+    information = information
   ))
 }
 
@@ -387,8 +385,7 @@ SpatialFeaturePlot <- function(
   shape = 21,
   stroke = NA,
   interactive = FALSE,
-  information = NULL,
-  plot_segmentations = FALSE
+  information = NULL
 ) {
   return(SpatialPlot(
     object = object,
@@ -408,8 +405,7 @@ SpatialFeaturePlot <- function(
     shape = shape,
     stroke = stroke,
     interactive = interactive,
-    information = information,
-    plot_segmentations = plot_segmentations
+    information = information
   ))
 }