Merge pull request #82 from vitessce/keller-mark/refactoring

Refactor into two packages

.gitignore

@@ -10,4 +10,5 @@ data/
 check/
 vignettes/data/
 *.Rproj
-.RData
+.RData
+my_vitessce_files/

DESCRIPTION

@@ -14,11 +14,10 @@ Authors@R: c(
 Description:
   R API and htmlwidget facilitating interactive visualization
   of spatial single-cell data with Vitessce. The R API contains
-  classes and functions for loading single-cell data stored as
-  SingleCellExperiment, SpatialExperiment, and Seurat objects.
-  The htmlwidget is a wrapper around the Vitessce JavaScript
-  library and can be used in the Viewer tab of RStudio or Shiny
-  apps.
+  classes and functions for loading single-cell data stored in
+  compatible on-disk formats. The htmlwidget is a wrapper around
+  the Vitessce JavaScript library and can be used in the Viewer tab
+  of RStudio or Shiny apps.
 biocViews: SingleCell, Spatial, Visualization, ShinyApps
 License: MIT + file LICENSE
 BugReports: https://github.com/vitessce/vitessceR/issues
@@ -37,21 +36,16 @@ Imports:
     jsonlite,
     R6,
     plumber,
+    mime,
     future,
     httpuv,
     stringr,
-    reticulate,
-    varhandle,
+    stringi,
     tools,
     stats,
     methods,
     S4Vectors,
-    grDevices,
-    basilisk,
-    zellkonverter,
-    SummarizedExperiment,
-    SingleCellExperiment,
-    SpatialExperiment
+    grDevices
 Suggests: 
     testthat,
     knitr,
@@ -60,7 +54,4 @@ Suggests:
     pkgdown,
     rmarkdown,
     purrr,
-    rjson,
-    Seurat,
-    SeuratDisk,
-    Giotto
+    rjson

LICENSE

@@ -1,2 +1,2 @@
 YEAR: 2020
-COPYRIGHT HOLDER: Gehlenborg Lab
+COPYRIGHT HOLDER: HIDIVE Lab

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2020 Gehlenborg Lab
+Copyright (c) 2020 HIDIVE Lab
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NAMESPACE

@@ -1,44 +1,20 @@
 # Generated by roxygen2: do not edit by hand
 
 export(AbstractWrapper)
+export(AnnDataWrapper)
 export(Component)
 export(CoordinationType)
+export(CsvWrapper)
 export(DataType)
 export(FileType)
-export(GiottoWrapper)
 export(MultiImageWrapper)
 export(OmeTiffWrapper)
-export(SCEWrapper)
-export(SPEWrapper)
-export(SeuratWrapper)
 export(VitessceConfig)
-export(get_giotto_obj)
-export(get_sce_obj)
-export(get_seurat_obj)
-export(get_spe_obj)
-export(giotto_to_anndata_zarr)
 export(hconcat)
 export(obj_list)
 export(render_vitessce)
-export(sce_to_anndata_zarr)
-export(seurat_to_anndata_zarr)
-export(spe_to_anndata_zarr)
-export(spe_to_ome_zarr)
 export(vconcat)
 export(vitessce_output)
 export(vitessce_widget)
 import(R6)
 import(plumber)
-importFrom(SingleCellExperiment,"reducedDims<-")
-importFrom(SingleCellExperiment,int_colData)
-importFrom(SingleCellExperiment,reducedDims)
-importFrom(SpatialExperiment,"colData<-")
-importFrom(SpatialExperiment,getImg)
-importFrom(SummarizedExperiment,colData)
-importFrom(grDevices,as.raster)
-importFrom(grDevices,col2rgb)
-importFrom(methods,new)
-importFrom(methods,slot)
-importFrom(stats,rnorm)
-importFrom(stats,rpois)
-importFrom(stats,runif)