Reapply "Merge branch 'dev' into dev2"

This reverts commit 961dc22.
drieslab · May 28, 2024 · 13e9fcb · 13e9fcb
1 parent 961dc22
commit 13e9fcb
Show file tree

Hide file tree

Showing 29 changed files with 50 additions and 30 deletions.
diff --git a/.github/workflows/dev_check.yml b/.github/workflows/dev_check.yml
@@ -45,6 +45,7 @@ jobs:
             any::ggalluvial
             any::ggforce
             any::ggraph
+            any::hexbin
 
       - name: Set up dependencies (GiottoUtils)
         run: |

diff --git a/R/vis_spatial.R b/R/vis_spatial.R
@@ -771,6 +771,15 @@ spatPlot2D <- function(
 #'     color_as_factor = FALSE,
 #'     gradient_style = "sequential"
 #' )
+#'
+#'
+#' # load another dataset with 3D data
+#' starmap <- GiottoData::loadGiottoData("starmap", verbose = FALSE)
+#'
+#' # default is to rescale plot as a 3D cube
+#' spatPlot3D(starmap, cell_color = "leiden_clus")
+#' # real scaling
+#' spatPlot3D(g, cell_color = "leiden_clus", axis_scale = "real")
 #' @export
 #' @seealso \code{\link{spatPlot3D}}
 spatPlot <- function(...) {
@@ -5251,7 +5260,7 @@ dimPlot3D <- function(gobject,
 #' @returns plotly
 #' @examples
 #' g <- GiottoData::loadGiottoMini("starmap")
-#' plotUMAP_3D(g)
+#' plotUMAP_3D(g, dim_reduction_name = "3D_umap")
 #'
 #' @export
 plotUMAP_3D <- function(gobject,

diff --git a/R/vis_spatial_in_situ.R b/R/vis_spatial_in_situ.R
@@ -636,6 +636,7 @@ spatInSituPlotHex <- function(
         polygon_line_size <- polygon_size
     }
 
+    package_check("hexbin")
 
     if (is.null(feats)) {
         stop("You need to select features (feats) and modify

diff --git a/man/addGiottoImageToSpatPlot.Rd b/man/addGiottoImageToSpatPlot.Rd
diff --git a/man/create_cluster_dendrogram.Rd b/man/create_cluster_dendrogram.Rd
diff --git a/man/dimCellPlot.Rd b/man/dimCellPlot.Rd
diff --git a/man/dimFeatPlot2D.Rd b/man/dimFeatPlot2D.Rd
diff --git a/man/dimPlot.Rd b/man/dimPlot.Rd
diff --git a/man/plotHeatmap.Rd b/man/plotHeatmap.Rd
diff --git a/man/plotMetaDataHeatmap.Rd b/man/plotMetaDataHeatmap.Rd
diff --git a/man/plotPCA.Rd b/man/plotPCA.Rd
diff --git a/man/plotPCA_2D.Rd b/man/plotPCA_2D.Rd
diff --git a/man/plotTSNE.Rd b/man/plotTSNE.Rd
diff --git a/man/plotTSNE_2D.Rd b/man/plotTSNE_2D.Rd
diff --git a/man/plotUMAP.Rd b/man/plotUMAP.Rd
diff --git a/man/plotUMAP_2D.Rd b/man/plotUMAP_2D.Rd
diff --git a/man/plotUMAP_3D.Rd b/man/plotUMAP_3D.Rd
diff --git a/man/plotly_grid.Rd b/man/plotly_grid.Rd
diff --git a/man/showClusterDendrogram.Rd b/man/showClusterDendrogram.Rd
diff --git a/man/showClusterHeatmap.Rd b/man/showClusterHeatmap.Rd
diff --git a/man/spatCellPlot.Rd b/man/spatCellPlot.Rd
diff --git a/man/spatDimCellPlot.Rd b/man/spatDimCellPlot.Rd
diff --git a/man/spatDimCellPlot2D.Rd b/man/spatDimCellPlot2D.Rd
diff --git a/man/spatDimFeatPlot2D.Rd b/man/spatDimFeatPlot2D.Rd
diff --git a/man/spatDimPlot.Rd b/man/spatDimPlot.Rd
diff --git a/man/spatFeatPlot2D.Rd b/man/spatFeatPlot2D.Rd
diff --git a/man/spatFeatPlot2D_single.Rd b/man/spatFeatPlot2D_single.Rd
diff --git a/man/spatPlot.Rd b/man/spatPlot.Rd
diff --git a/man/violinPlot.Rd b/man/violinPlot.Rd