Merge pull request #536 from drieslab/suite_dev

3.2 patches

NAMESPACE

@@ -412,6 +412,7 @@ export(trendSceek)
 export(updateGiottoImage)
 export(updateGiottoImageMG)
 export(updateGiottoLargeImage)
+export(updateGiottoObject)
 export(validObject)
 export(viewHMRFresults)
 export(viewHMRFresults2D)

NEWS.md

@@ -14,6 +14,7 @@
 - New `createSpatialWeightMatrix()` function to generate spatial weight matrix from spatial networks for autocorrelation
 - Add spatial_interaction_spot.R with functions adapted from master branch for working with the Giotto suite object.
 - New exported accessors for slots (experimental)
+- New `multiomics` slot in `giotto`
 - Add `coord_fix_ratio` param to `spatFeatPlot2D()` and `spatFeatPlot2D_single()`
 - Add `order` parameter to `dimFeatPlot2D` and `spatDimFeatPlot2d` to plot and order cells according to the levels of the selected feature ([#477](https://github.com/drieslab/Giotto/issues/477))
 - Add `plot()` method for `spatialNetworkObj`

R/classes.R

@@ -381,15 +381,39 @@ setClass('spatFeatData',
 #             .Object
 #           })
 
-# TODO
-# updateGiottoObject = function(gobject) {
-#   if(is.null(attr(gobject, 'multiomics'))) {
-#     attr(gobject, 'multiomics') = NA
-#     gobject@multiomics = NULL
-#   }
-#
-#   return(gobject)
-# }
+
+
+
+
+#' @title Update giotto object
+#' @name updateGiottoObject
+#' @description Updates the giotto object for changes in structure for backwards
+#' compatibility with earlier versions
+#' @param gobject giotto object to update
+#' @details
+#' Supported updates:
+#' \itemize{
+#'   \item{3.2.0 update adding multiomics slot}
+#'   \item{master branch to suite - TODO}
+#' }
+#' @usage gobject = updateGiottoObject(gobject)
+#' @export
+updateGiottoObject = function(gobject) {
+
+  if(!inherits(gobject, 'giotto')) {
+    stop(wrap_txt('This function is intended for updating giotto objects'))
+  }
+
+  # 3.2.0 release adds multiomics slot
+  if(is.null(attr(gobject, 'multiomics'))) {
+    attr(gobject, 'multiomics') = NA
+    gobject@multiomics = NULL
+  }
+
+  return(gobject)
+}
+
+
 
 ##### * Definition ####
 # Giotto class

R/general_help.R

@@ -696,12 +696,15 @@ sort_combine_two_DT_columns = function(DT,
 check_github_suite_ver = function() {
   current_ver = utils::packageVersion('Giotto')
   url = paste0('https://raw.githubusercontent.com/drieslab/Giotto/suite/DESCRIPTION')
-  x = readLines(url)
-  gh_ver = x[grep(pattern = 'Version:', x)]
-  gh_ver = gsub(pattern = 'Version: ', replacement = '', gh_ver)
-  ver_compare = utils::compareVersion(gh_ver, as.character(current_ver))
-
-  if(ver_compare == 1) wrap_msg('Newer devel version of Giotto on GitHub:', gh_ver)
+  # suppress warnings and errors if inaccessible
+  x = suppressWarnings(try(readLines(url), silent = TRUE))
+  if(!inherits(x, 'try-error')) {
+    gh_ver = x[grep(pattern = 'Version:', x)]
+    gh_ver = gsub(pattern = 'Version: ', replacement = '', gh_ver)
+    ver_compare = utils::compareVersion(gh_ver, as.character(current_ver))
+
+    if(ver_compare == 1) wrap_msg('Newer devel version of Giotto on GitHub:', gh_ver)
+  }
 }