couple copi fixes

DESCRIPTION

@@ -3,7 +3,7 @@ Title: Representation of Python's SpatialData in R
 Depends: R (>= 4.5)
 Version: 0.99.25
 Description: Interface to Python's 'SpatialData', currently including:
-    reticulate-based use of 'spatialdata-io' for reading of manufracturer
+    reticulate-based use of 'spatialdata-io' for reading of manufacturer
     data and writing to .zarr, on-disk representation of images/labels as
     'ZarrArray's ('Rarr') and shapes/points as 'arrow' objects, and method 
     drafts for visualization and coordinate system handling.

R/AllGenerics.R

@@ -22,18 +22,6 @@ setGeneric("shapeNames", \(x, ...) standardGeneric("shapeNames"))
 setGeneric("pointNames", \(x, ...) standardGeneric("pointNames"))
 setGeneric("tableNames", \(x, ...) standardGeneric("tableNames"))
 
-setMethod("images", "SpatialData", \(x) x$images)
-setMethod("labels", "SpatialData", \(x) x$labels)
-setMethod("shapes", "SpatialData", \(x) x$shapes)
-setMethod("points", "SpatialData", \(x) x$points)
-setMethod("tables", "SpatialData", \(x) x$tables)
-
-setMethod("imageNames", "SpatialData", \(x) names(images(x)))
-setMethod("labelNames", "SpatialData", \(x) names(labels(x)))
-setMethod("shapeNames", "SpatialData", \(x) names(shapes(x)))
-setMethod("pointNames", "SpatialData", \(x) names(points(x)))
-setMethod("tableNames", "SpatialData", \(x) names(tables(x)))
-
 # set one -----
 
 setGeneric("image<-", \(x, i, ..., value) standardGeneric("image<-"))

R/ShapeFrame.R

@@ -82,7 +82,7 @@ setMethod("[", c("ShapeFrame", "missing", "missing"),
 #' @export
 setMethod("[", c("ShapeFrame", "numeric", "numeric"), \(x, i, j, ...) { 
     i <- seq_len(nrow(x))[i]
-    j <- seq_len(nrow(x))[j]
+    j <- seq_len(ncol(x))[j]
     x@data <- x@data[i, j]
     return(x)
 })

R/coord_utils.R

@@ -247,7 +247,7 @@ setMethod("rmvCT", "Zattrs", \(x, i) {
     }
     nan <- setdiff(i, nms)
     if (length(nan)) stop(
-        "couln't find 'coordTrans' of name(s) ", 
+        "couldn't find 'coordTrans' of name(s) ", 
         paste(dQuote(nan), collapse=","))
     i <- match(i, nms)
     # protect against dropping identity

R/read.R

@@ -211,7 +211,7 @@ readSpatialData <- function(x,
             if (is.numeric(opt) && opt > (. <- length(j))) 
                 stop("'", i, "=", opt, "', but only ", ., " elements found")
             if (is.character(opt) && length(. <- setdiff(opt, basename(j))))
-                stop("couln't find ", i, " of name", .)
+                stop("couldn't find ", i, " of name", .)
             j <- j[opt]
         }
         f <- get(paste0("read", toupper(substr(i, 1, 1)), substr(i, 2, nchar(i)-1)))

R/validity.R

@@ -38,9 +38,9 @@
 .validateImageArray <- function(object) {
     msg <- c()
     if (ni <- length(images(object))) {
-        for (i in seq_along(ni)) {
+        for (i in seq_len(ni)) {
             ai <- as.array(aperm(data(image(object,1))/255, perm=c(3,2,1)))
-            for (j in dim(ai)[3]) {
+            for (j in seq_len(dim(ai)[3])) {
                 if (!all(vapply(ai[,,j], is.numeric, logical(1)))) {
                     msg <- c(msg, paste0("Image ", i, " channel ", j, " not numeric"))
                 }