update docs, cran checks

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
 Version: 4.2.1.9000
-Date: 2022-11-07
+Date: 2022-11-09
 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(
@@ -24,7 +24,6 @@ Authors@R: c(
   )
 URL: https://satijalab.org/seurat, https://github.com/satijalab/seurat
 BugReports: https://github.com/satijalab/seurat/issues
-Remotes: mojaveazure/seurat-object@develop
 Depends:
     R (>= 4.0.0),
     methods
@@ -67,13 +66,8 @@ Imports:
     Rtsne,
     scales,
     scattermore (>= 0.7),
-<<<<<<< HEAD
-    sctransform (>= 0.3.4),
-    SeuratObject (>= 4.1.2.9003),
-=======
     sctransform (>= 0.3.5),
     SeuratObject (>= 4.1.3),
->>>>>>> develop
     shiny,
     spatstat.explore,
     spatstat.geom,

NAMESPACE

@@ -426,7 +426,6 @@ importFrom(SeuratObject,"Misc<-")
 importFrom(SeuratObject,"Project<-")
 importFrom(SeuratObject,"Tool<-")
 importFrom(SeuratObject,"VariableFeatures<-")
-importFrom(SeuratObject,.DefaultFOV)
 importFrom(SeuratObject,AddMetaData)
 importFrom(SeuratObject,Assays)
 importFrom(SeuratObject,AttachDeps)
@@ -443,6 +442,7 @@ importFrom(SeuratObject,CreateSeuratObject)
 importFrom(SeuratObject,DefaultAssay)
 importFrom(SeuratObject,DefaultBoundary)
 importFrom(SeuratObject,DefaultDimReduc)
+importFrom(SeuratObject,DefaultFOV)
 importFrom(SeuratObject,Distances)
 importFrom(SeuratObject,Embeddings)
 importFrom(SeuratObject,Features)
@@ -640,6 +640,7 @@ importFrom(matrixStats,rowSums2)
 importFrom(methods,"slot<-")
 importFrom(methods,.hasSlot)
 importFrom(methods,as)
+importFrom(methods,getMethod)
 importFrom(methods,is)
 importFrom(methods,new)
 importFrom(methods,setAs)

R/preprocessing.R

@@ -7,6 +7,11 @@ NULL
 # Functions
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
+globalVariables(
+  names = c('fov', 'cell_ID'),
+  package = 'Seurat',
+  add = TRUE
+)
 #' Calculate the Barcode Distribution Inflection
 #'
 #' This function calculates an adaptive inflection point ("knee") of the barcode distribution
@@ -1591,6 +1596,11 @@ ReadMtx <- function(
 #'  \item \dQuote{centroids}: cell centroids in pixel coordinate space
 #'  \item \dQuote{segmentations}: cell segmentations in pixel coordinate space
 #' }
+#' @param mol.type Type of molecule spatial coordinate matrices to read;
+#' choose one or more of:
+#' \itemize{
+#'  \item \dQuote{pixels}: molecule coordinates in pixel space
+#' }
 #' @param metadata Type of available metadata to read;
 #' choose zero or more of:
 #' \itemize{
@@ -2040,9 +2050,12 @@ ReadSlideSeq <- function(coord.file, assay = 'Spatial') {
 #' @examples
 #' \dontrun{
 #' coords <- ReadVitessce(
-#'   counts = "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/wang/wang.genes.json",
-#'   coords = "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/wang/wang.cells.json",
-#'   molecules = "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/wang/wang.molecules.json"
+#'   counts =
+#'      "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/wang/wang.genes.json",
+#'   coords =
+#'      "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/wang/wang.cells.json",
+#'   molecules =
+#'      "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/wang/wang.molecules.json"
 #' )
 #' names(coords)
 #' coords$counts[1:10, 1:10]

R/visualization.R

@@ -2270,24 +2270,25 @@ PolyFeaturePlot <- function(
 #' Names should be the names of FOVs and values should be the names of
 #' segmentation boundaries
 #' @param molecules A vector of molecules to plot
+#' @param nmols Max number of each molecule specified in `molecules` to plot
 #' @param dark.background Set plot background to black
 #' @param crop Crop the plots to area with cells only
 #' @param overlap Overlay boundaries from a single image to create a single
 #' plot; if \code{TRUE}, then boundaries are stacked in the order they're
 #' given (first is lowest)
 #' @param axes Keep axes and panel background
 #' @param combine Combine plots into a single
-#' \code{\link[patchwork]{patchworked}} ggplot object.If \code{FALSE},
+#' \code{patchwork} ggplot object.If \code{FALSE},
 #' return a list of ggplot objects
 #' @param coord.fixed Plot cartesian coordinates with fixed aspect ratio
 #'
-#' @return If \code{combine = TRUE}, a \code{\link[patchwork]{patchwork}ed}
+#' @return If \code{combine = TRUE}, a \code{patchwork}
 #' ggplot object; otherwise, a list of ggplot objects
 #'
 #' @importFrom rlang !! is_na sym
 #' @importFrom patchwork wrap_plots
 #' @importFrom ggplot2 element_blank facet_wrap vars
-#' @importFrom SeuratObject .DefaultFOV Cells
+#' @importFrom SeuratObject DefaultFOV Cells
 #' DefaultBoundary FetchData Images Overlay
 #'
 #' @export
@@ -2513,7 +2514,7 @@ ImageDimPlot <- function(
 #' @importFrom cowplot theme_cowplot
 #' @importFrom ggplot2 dup_axis element_blank element_text facet_wrap guides
 #' labs margin vars scale_y_continuous theme
-#' @importFrom SeuratObject .DefaultFOV Cells DefaultBoundary
+#' @importFrom SeuratObject DefaultFOV Cells DefaultBoundary
 #' FetchData Images Overlay
 #'
 #' @export
@@ -2548,8 +2549,7 @@ ImageFeaturePlot <- function(
   overlap = FALSE,
   axes = FALSE,
   combine = TRUE,
-  coord.fixed = TRUE,
-  ...
+  coord.fixed = TRUE
 ) {
   cells <- cells %||% Cells(x = object)
   scale <- scale[[1L]]
@@ -4681,10 +4681,10 @@ PlotClusterTree <- function(object, direction = "downwards", ...) {
 #' @param balanced Return an equal number of genes with + and - scores. If
 #' FALSE (default), returns the top genes ranked by the scores absolute values
 #' @param ncol Number of columns to display
-#' @param combine Combine plots into a single \code{\link[patchwork]{patchwork}ed}
+#' @param combine Combine plots into a single \code{patchwork}
 #' ggplot object. If \code{FALSE}, return a list of ggplot objects
 #'
-#' @return A \code{\link[patchwork]{patchwork}ed} ggplot object if
+#' @return A \code{patchwork} ggplot object if
 #' \code{combine = TRUE}; otherwise, a list of ggplot objects
 #'
 #' @importFrom patchwork wrap_plots
@@ -6137,9 +6137,9 @@ WhiteBackground <- function(...) {
 #' Prepare Coordinates for Spatial Plots
 #'
 #' @inheritParams SeuratObject::GetTissueCoordinates
-#' @param model A \code{\link{[SeuratObject:Segmentation-class]Segmentation}},
-#' \code{\link[SeuratObject:Centroids-class]{Centroids}},
-#' or \code{\link[SeuratObject:Molecules-class]{Molecules}} object
+#' @param model A \code{\linkS4class{Segmentation}},
+#' \code{\linkS4class{Centroids}},
+#' or \code{\linkS4class{Molecules}} object
 #' @param data Extra data to be used for annotating the cell segmentations; the
 #' easiest way to pass data is a one-column
 #' \code{\link[base:data.frame]{data frame}} with the values to color by and
@@ -6182,26 +6182,7 @@ fortify.Molecules <- function(
   seed = NA_integer_,
   ...
 ) {
-  return(FetchData(object = object, vars = data, nmols = nmols, seed = seed, ...))
-  # coords <- GetTissueCoordinates(object = model, features = data)
-  # if (!is.null(x = nmols)) {
-  #   if (!is.na(x = seed)) {
-  #     set.seed(seed = seed)
-  #   }
-  #   coords <- lapply(
-  #     X = unique(x = coords$molecule),
-  #     FUN = function(m) {
-  #       df <- coords[coords$molecule == m, , drop = FALSE]
-  #       if (nrow(x = df) > nmols) {
-  #         idx <- sample(x = seq_len(length.out = nrow(x = df)), size = nmols)
-  #         df <- df[idx, , drop = FALSE]
-  #       }
-  #       return(df)
-  #     }
-  #   )
-  #   coords <- do.call(what = 'rbind', args = coords)
-  # }
-  # return(coords)
+  return(FetchData(object = model, vars = data, nmols = nmols, seed = seed, ...))
 }
 
 #' @rdname fortify-Spatial
@@ -8977,6 +8958,7 @@ setMethod(
   }
 )
 
+#' @importFrom methods getMethod
 setMethod(
   f = '.PrepImageData',
   signature = c(data = 'factor', cells = 'rle'),
@@ -9001,7 +8983,7 @@ setMethod(
   f = '.PrepImageData',
   signature = c(data = 'NULL', cells = 'rle'),
   definition = function(data, cells, ...) {
-    return(SeuratObject:::EmptyDF(n = sum(cells$lengths)))
+    return(SeuratObject::EmptyDF(n = sum(cells$lengths)))
   }
 )