Pass R CMD check on my machine

Author: lambdamoses

DESCRIPTION

@@ -1,11 +1,14 @@
 Package: Voyager
 Type: Package
 Title: From geospatial to spatial omics
-Version: 1.5.0
+Version: 1.5.1
 Authors@R: 
     c(person("Lambda", "Moses", email = "[email protected]", 
     role = c("aut", "cre"),
     comment = c(ORCID = "0000-0002-7092-9427")),
+    person("Alik", "Huseynov",
+    comment = c(ORCID = "0000-0002-1438-4389"),
+    role = "aut"),
     person("Kayla", "Jackson", email = "[email protected]",
     role = c("aut"),
     comment = c(ORCID = "0000-0001-6483-0108")),

NAMESPACE

@@ -78,6 +78,7 @@ importFrom(RSpectra,eigs_sym)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,Rle)
+importFrom(S4Vectors,combineCols)
 importFrom(S4Vectors,make_zero_col_DFrame)
 importFrom(S4Vectors,metadata)
 importFrom(SingleCellExperiment,"int_colData<-")
@@ -106,10 +107,13 @@ importFrom(SpatialFeatureExperiment,colFeatureData)
 importFrom(SpatialFeatureExperiment,colGeometry)
 importFrom(SpatialFeatureExperiment,colGraph)
 importFrom(SpatialFeatureExperiment,colGraphs)
+importFrom(SpatialFeatureExperiment,cropImg)
 importFrom(SpatialFeatureExperiment,df2sf)
 importFrom(SpatialFeatureExperiment,ext)
 importFrom(SpatialFeatureExperiment,geometryFeatureData)
+importFrom(SpatialFeatureExperiment,getParams)
 importFrom(SpatialFeatureExperiment,getPixelSize)
+importFrom(SpatialFeatureExperiment,imageIDs)
 importFrom(SpatialFeatureExperiment,imgSource)
 importFrom(SpatialFeatureExperiment,isFull)
 importFrom(SpatialFeatureExperiment,localResult)
@@ -120,6 +124,8 @@ importFrom(SpatialFeatureExperiment,rowGeometry)
 importFrom(SpatialFeatureExperiment,sampleIDs)
 importFrom(SpatialFeatureExperiment,spatialGraph)
 importFrom(SpatialFeatureExperiment,spatialGraphs)
+importFrom(SpatialFeatureExperiment,toSpatRasterImage)
+importFrom(SpatialFeatureExperiment,translateImg)
 importFrom(SummarizedExperiment,"colData<-")
 importFrom(SummarizedExperiment,"rowData<-")
 importFrom(SummarizedExperiment,assay)
@@ -212,6 +218,7 @@ importFrom(sf,st_drop_geometry)
 importFrom(sf,st_geometry)
 importFrom(sf,st_geometry_type)
 importFrom(sf,st_intersection)
+importFrom(sf,st_sfc)
 importFrom(spdep,card)
 importFrom(spdep,include.self)
 importFrom(spdep,listw2mat)

NEWS.md

@@ -1,6 +1,10 @@
-# Version 1.5.1
+# Version 1.6.0 (04/29/2023)
 * Option to plot polygon geometry without fill in plotGeometry
 * Option to show axes in both light and dark themes
+* Plot images of classes BioFormatsImage and ExtImage
+* Colorize image plot with different channels
+* Assign different grayscale images to channels
+* Added plotImage to only plot image without plotting geometry
 
 # Version 1.3.1 (05/15/2023)
 * Removed functions and arguments deprecated in 1.2.0

R/featureData.R

@@ -92,7 +92,7 @@
     fd
 }
 
-#' @importFrom S4Vectors metadata metadata<-
+#' @importFrom S4Vectors metadata metadata<- combineCols
 .initialize_fd_dimData <- function(x, MARGIN) {
     fd_name <- "featureData"
     dimData <- switch(MARGIN, rowData, colData)
@@ -103,7 +103,7 @@
         # Remove rows that correspond to columns that have been deleted and add
         # new ones
         fd <- metadata(dimData(x))[[fd_name]]
-        fd <- fd[intersect(rownames(fd), colnames(dimData(x))),]
+        fd <- fd[intersect(rownames(fd), colnames(dimData(x))),, drop = FALSE]
         empty <- .initDF(dimData(x))
         fd <- combineCols(empty, fd)
         metadata(dimData(x))[[fd_name]] <- fd

R/plot.R

@@ -465,7 +465,7 @@ getDivergeRange <- function(values, diverge_center = 0) {
 }
 
 #' @importFrom SpatialFeatureExperiment isFull imgSource getPixelSize ext
-#' aggBboxes
+#' aggBboxes cropImg imageIDs translateImg toSpatRasterImage getParams
 #' @importFrom sf st_area
 #' @importFrom terra RGB<- rast
 .find_res <- function(bfi, maxcell) {
@@ -498,7 +498,7 @@ getDivergeRange <- function(values, diverge_center = 0) {
 .get_n_channels <- function(img) {
     d <- dim(img)
     if (length(d) == 2L) return(1L)
-    d[[3]]
+    as.integer(d[[3]])
 }
 # What I want: option to assign individual grayscale images to different channels
 # Option to select one or more channels from a multi-channel image
@@ -507,7 +507,7 @@ getDivergeRange <- function(values, diverge_center = 0) {
     # BioFormatsImage
     # choose highest resolution with fewer than maxcell when multiple res are present
     # Convert to spi
-    # EBImage: convert to spi so can use custom color map in terra::as.raster
+    # ExtImage: convert to spi so can use custom color map in terra::as.raster
     # Combine different image classes: all use spi
     # For testing, need to use xenium v2 example data, everything is connected
     # All convert to spi, find the one with the lowest resolution, then
@@ -622,7 +622,7 @@ getDivergeRange <- function(values, diverge_center = 0) {
                 tot_area <- ext(x) |> st_bbox() |> st_as_sfc() |> st_area()
                 bb_area <- bbox |> st_bbox() |> st_as_sfc() |> st_area()
                 bb_prop <- bb_area/tot_area
-                if (!inMemory(x)) {
+                if (!terra::inMemory(x)) {
                     # Shouldn't need to write the cropped part to disk just for a plot
                     tot_size <- file.info(imgSource(x))$size
                     mem_free <- Sys.meminfo()$freeram |> as.numeric()
@@ -646,7 +646,7 @@ getDivergeRange <- function(values, diverge_center = 0) {
         if (is(img, "BioFormatsImage")) {
             res_use <- .find_res(img, maxcell)
             spi <- toSpatRasterImage(img, resolution = res_use, save_geotiff = FALSE)
-        } else if (is(img, "EBImage")) {
+        } else if (is(img, "ExtImage")) {
             spi <- toSpatRasterImage(img, save_geotiff = FALSE)
         } else spi <- img
         spi |> resample_spat(maxcell)
@@ -1071,7 +1071,7 @@ plotSpatialFeature <- function(sfe, features, colGeometryName = 1L,
 #' @importFrom SpatialExperiment spatialCoords
 #' @importFrom SpatialFeatureExperiment spatialGraphs spatialGraph
 #' @importFrom spdep card
-#' @importFrom sf st_coordinates st_centroid st_geometry
+#' @importFrom sf st_coordinates st_centroid st_geometry st_sfc
 #' @return A ggplot2 object.
 #' @export
 #' @concept Spatial plotting