Merge branch 'devel' of https://github.com/pachterlab/voyager into devel

R/SFEMethod-bivariate.R

@@ -12,7 +12,7 @@
 #' @importFrom DelayedArray sweep
 .lee_mat <- function(x, y = NULL, listw, zero.policy = TRUE, ...) {
     # X has genes in rows
-    if (is(listw, "listw"))
+    if (inherits(listw, "listw"))
         W <- listw2sparse(listw)
     else W <- listw
     x <- .scale_n(x)

R/SFEMethod-multivariate.R

@@ -52,15 +52,15 @@ multispati_rsp <- function(x, listw, nfposi = 30L, nfnega = 30L, scale = TRUE) {
         stop("At least one of nfposi and nfnega must be positive.")
     }
     x <- sweep(x, 2, colMeans(x))
-    if (is(x, "dgeMatrix")) x <- as.matrix(x)
+    if (inherits(x, "dgeMatrix")) x <- as.matrix(x)
     if (scale) {
         # Note that dudi.pca divides by n instead of n-1 when scaling data
         n <- nrow(x)
         x <- sweep(x, 2, sqrt(matrixStats::colVars(x)*(n-1)/n), FUN = "/")
     }
     if (inherits(listw, "Matrix") || is.matrix(listw))
         W <- listw
-    else if (is(listw, "listw"))
+    else if (inherits(listw, "listw"))
         W <- listw2sparse(listw)
     else
         stop("listw must be either a listw object or an adjacency matrix.")

R/bivariate.R

@@ -148,7 +148,7 @@ setMethod("calculateBivariate", "ANY",
                       out <- reorganize_fun(type)(out, name = name, ...)
                   }
               }
-              if (length(out) == 1L && !is(out, "DataFrame")) out <- out[[1]]
+              if (length(out) == 1L && !inherits(out, "DataFrame")) out <- out[[1]]
               out
           })
 

R/multivariate.R

@@ -178,7 +178,7 @@ setMethod("calculateMultivariate", "SpatialFeatureExperiment",
 
                       is_vector <- all(vapply(out, is.vector, FUN.VALUE = logical(1)))
                       is_matrix <- all(vapply(out, is.matrix, FUN.VALUE = logical(1)))
-                      is_df <- all(vapply(out, function(o) is.data.frame(o) | is(o, "DataFrame"),
+                      is_df <- all(vapply(out, function(o) is.data.frame(o) | inherits(o, "DataFrame"),
                                           FUN.VALUE = logical(1)))
                       if (is_vector) {
                           out <- unlist(out)
@@ -223,7 +223,7 @@ runMultivariate <- function(x, type, colGraphName = 1L,
         reducedDim(x, name) <- out
     } else {
         if (is.vector(out)) colData(x)[[name]] <- out
-        if (is.data.frame(out) || is(out, "DataFrame")) {
+        if (is.data.frame(out) || inherits(out, "DataFrame")) {
             inds <- !grepl(name, names(out))
             names(out)[inds] <- paste(name, names(out)[inds], sep = "_")
             colData(x) <- cbind(colData(x), out)

R/plot-univar-downstream.R

@@ -38,7 +38,7 @@
             warning("Too few points for stat_density2d, not plotting contours.")
         }
     )
-    if (is(p_test, "ggplot_built")) {
+    if (inherits(p_test, "ggplot_built")) {
         p <- p + geom_density2d(color = contour_color, bins = bins, ...)
     }
     p <- p +

R/plot.R

@@ -412,7 +412,7 @@ getDivergeRange <- function(values, diverge_center = 0) {
 
 #' @importFrom sf st_as_sfc st_bbox st_intersection
 .bbox_sample <- function(df, bbox) {
-    if (is(df, "sf")) {
+    if (inherits(df, "sf")) {
         # Only for one sample
         bbox_use <- st_as_sfc(st_bbox(bbox))
         suppressWarnings(df <- st_intersection(df, bbox_use))
@@ -659,7 +659,7 @@ getDivergeRange <- function(values, diverge_center = 0) {
         # the bbox is a large part of the image that also needs to be written to
         # disk
         imgs <- lapply(imgs, function(x) {
-            if (is(x, "SpatRasterImage")) {
+            if (inherits(x, "SpatRasterImage")) {
                 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
@@ -684,10 +684,10 @@ getDivergeRange <- function(values, diverge_center = 0) {
     }
     # All convert to SpatRaster
     imgs <- lapply(imgs, function(img) {
-        if (is(img, "BioFormatsImage")) {
+        if (inherits(img, "BioFormatsImage")) {
             res_use <- .find_res(img, maxcell)
             spi <- toSpatRasterImage(img, resolution = res_use, save_geotiff = FALSE)
-        } else if (is(img, "ExtImage")) {
+        } else if (inherits(img, "ExtImage")) {
             spi <- toSpatRasterImage(img, save_geotiff = FALSE)
         } else spi <- img
         spi |> resample_spat(maxcell)
@@ -772,7 +772,7 @@ getDivergeRange <- function(values, diverge_center = 0) {
         img_df <- .get_img_df(sfe, sample_id, image_id, channel, bbox, maxcell,
                               normalize_channels)
     } else img_df <- NULL
-    if (is(img_df, "DataFrame") && !nrow(img_df)) img_df <- NULL
+    if (inherits(img_df, "DataFrame") && !nrow(img_df)) img_df <- NULL
     .wrap_spatial_plots(
         df, annot_df, img_df, channel, type_annot, values, aes_use,
         annot_aes, annot_fixed, tx_fixed, size, shape, linewidth, linetype, alpha,

R/plotLocalResult.R

@@ -206,7 +206,7 @@ plotLocalResult <- function(sfe, name, features, attribute = NULL,
                                                       channel, bbox, maxcell,
                                                       normalize_channels)
         else img_df <- NULL
-        if (is(img_df, "DataFrame") && !nrow(img_df)) img_df <- NULL
+        if (inherits(img_df, "DataFrame") && !nrow(img_df)) img_df <- NULL
         if (!is.null(rowGeometryName)) {
             tx_df <- .get_tx_df(sfe, data_dir = NULL, tech = NULL, file = NULL,
                                 sample_id = sample_id, spatialCoordsNames = c("X", "Y"),
@@ -229,7 +229,7 @@ plotLocalResult <- function(sfe, name, features, attribute = NULL,
         )
     }
     # Add title to not to confuse with gene expression
-    if (is(out, "patchwork")) {
+    if (inherits(out, "patchwork")) {
         out <- out + plot_annotation(title = title_use)
     } else {
         out <- out + ggtitle(title_use)

R/plotSpatialReducedDim.R

@@ -75,7 +75,7 @@ spatialReducedDim <- function(sfe, dimred, ncomponents = NULL,
         normalize_channels = normalize_channels, rowGeometryName = rowGeometryName,
         rowGeometryFeatures = rowGeometryFeatures, tx_file = tx_file, ...
     )
-    if (is(out, "patchwork")) {
+    if (inherits(out, "patchwork")) {
         out <- out + plot_annotation(title = dimred)
     } else {
         out <- out + ggtitle(dimred)

R/univariate-internal.R

@@ -1,7 +1,7 @@
 # Internal function for univariate metrics
 .calc_univar <- function(x, fun, BPPARAM, ...) {
-    if (is(x, "DFrame") || is.data.frame(x)) {
-        if (is(x, "sf")) x <- st_drop_geometry(x)
+    if (inherits(x, "DFrame") || is.data.frame(x)) {
+        if (inherits(x, "sf")) x <- st_drop_geometry(x)
         x <- t(as.matrix(x))
         if (anyNA(x)) {
             stop("Only numeric columns without NA (within the sample_id) can be used.")
@@ -17,12 +17,12 @@
 #' @importFrom stats as.formula terms
 .get_coords_df <- function(x, df, sample_id, exprs_values,
                            swap_rownames, ...) {
-    if (!is(df, "sf") || st_geometry_type(df, by_geometry = FALSE) != "POINT") {
-        if (is(df, "sf")) df <- st_drop_geometry(df)
+    if (!inherits(df, "sf") || st_geometry_type(df, by_geometry = FALSE) != "POINT") {
+        if (inherits(df, "sf")) df <- st_drop_geometry(df)
         # Can't use list columns as regressors
         inds_keep <- vapply(df, is.atomic, FUN.VALUE = logical(1))
         df <- df[,inds_keep]
-        if (is(df, "DataFrame")) df <- as.data.frame(df)
+        if (inherits(df, "DataFrame")) df <- as.data.frame(df)
         colnames_use <- spatialCoordsNames(x)
         geo <- df2sf(spatialCoords(x)[x$sample_id == sample_id,], colnames_use)
         oth_names <- setdiff(names(df), colnames_use)

R/utils.R

@@ -195,7 +195,7 @@
 }
 
 .get_not_na_items <- function(df, features, colname_use) {
-    if (is(df, "sf")) df <- st_drop_geometry(df)
+    if (inherits(df, "sf")) df <- st_drop_geometry(df)
     if (!colname_use %in% names(df)) {
         return(NULL)
     }