Merge pull request #891 from drieslab/suite

Catch up to suite

.gitignore

@@ -13,8 +13,3 @@ testdata
 merfish_preoptic/
 
 *.DS_Store
-:temp:
-*.wal
-
-*.RDS
-*.db

R/auxiliary_giotto.R

@@ -18,7 +18,6 @@
   }))
 }
 
-
 #' @title Normalize expression matrix for library size
 #' @param mymatrix matrix object
 #' @param scalefactor scalefactor
@@ -32,16 +31,15 @@
                      This will likely result in normalization problems.
                      filter (filterGiotto) or impute (imputeGiotto) spatial units.'))
   }
-
-  norm_expr = t_flex(t_flex(mymatrix)/ libsizes)*scalefactor
 
+  norm_expr = t_flex(t_flex(mymatrix)/ libsizes)*scalefactor
   return(norm_expr)
 }
 
 #' @title Log normalize expression matrix
 #' @keywords internal
 .log_norm_giotto = function(mymatrix, base, offset) {
-  
+
   if(methods::is(mymatrix, 'DelayedArray')) {
     mymatrix = log(mymatrix + offset)/log(base)
     # } else if(methods::is(mymatrix, 'DelayedMatrix')) {
@@ -50,9 +48,6 @@
     mymatrix@x = log(mymatrix@x + offset)/log(base) # replace with sparseMatrixStats
   } else if(methods::is(mymatrix, 'Matrix')) {
     mymatrix@x = log(mymatrix@x + offset)/log(base)
-  } else if(methods::is(mymatrix, 'dbMatrix')) {
-    mymatrix[] = dplyr::mutate(mymatrix[], x = x + offset) # workaround for lack of @x slot
-    mymatrix = log(mymatrix)/log(base)
   } else {
     mymatrix = log(as.matrix(mymatrix) + offset)/log(base)
   }
@@ -518,13 +513,13 @@ filterGiotto = function(gobject,
   # 2. then remove cells that do not have sufficient detected genes
 
   ## filter features
-  filter_index_feats = GiottoClass::rowSums_flex(expr_values >= expression_threshold) >= feat_det_in_min_cells
+  filter_index_feats = rowSums_flex(expr_values >= expression_threshold) >= feat_det_in_min_cells
   selected_feat_ids = names(filter_index_feats[filter_index_feats == TRUE])
 
 
 
   ## filter cells
-  filter_index_cells = GiottoClass::colSums_flex(expr_values[filter_index_feats, ] >= expression_threshold) >= min_det_feats_per_cell
+  filter_index_cells = colSums_flex(expr_values[filter_index_feats, ] >= expression_threshold) >= min_det_feats_per_cell
   selected_cell_ids = names(filter_index_cells[filter_index_cells == TRUE])
 
 
@@ -652,7 +647,7 @@ filterGiotto = function(gobject,
   ## 1. library size normalize
   if(library_size_norm == TRUE) {
     norm_expr = .lib_norm_giotto(mymatrix = raw_expr[],
-                                 scalefactor = scalefactor)
+                               scalefactor = scalefactor)
   } else {
     norm_expr = raw_expr[]
   }

R/spatial_genes.R

@@ -1622,8 +1622,9 @@ silhouetteRank <- function(gobject,
 
   # expression values
   values = match.arg(expression_values, c('normalized', 'scaled', 'custom'))
-  expr_values = get_expression_values(gobject = gobject,
-                                      values = values)
+  expr_values = getExpression(gobject = gobject,
+                              values = values,
+                              output = "matrix")
 
   # subset genes
   if(!is.null(subset_genes)) {
@@ -1638,9 +1639,9 @@ silhouetteRank <- function(gobject,
 
   # spatial locations
   # spatlocs = as.matrix(gobject@spatial_locs[['cell']][['raw']][,.(sdimx, sdimy)])
-  spatlocs = get_spatial_locations(gobject,
+  spatlocs = getSpatialLocations(gobject,
                                    spat_unit = 'cell',
-                                   spat_loc_name = 'raw',
+                                   name = 'raw',
                                    output = 'data.table',
                                    copy_obj = TRUE)
   spatlocs = as.matrix(spatlocs[,.(sdimx, sdimy)])

R/spatial_interaction_visuals.R

@@ -2262,9 +2262,6 @@ plotRankSpatvsExpr = function(gobject,
     midpoint = gradient_midpoint,
     style = gradient_style,
     type = 'color',
-    type_default = list(
-      pal = c('blue', 'yellow', 'red')
-    ),
     guide = guide_legend(title = '')
   )
   pl = pl + ggplot2::scale_size_continuous(range = size_range, guide = "none")

_pkgdown.yml

@@ -92,6 +92,8 @@ navbar:
         href: articles/terra.html
       - text: Docker
         href: articles/docker.html
+      - text: Singularity
+        href: articles/singularity.html
     articles:
       text: Examples
       menu:
@@ -210,6 +212,7 @@ articles:
   contents:
   - terra
   - docker
+  - singularity
 - title: Spatial Manipulation
   navbar: ~
   contents: