v1.13.6 -- resolve #43

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: spatialLIBD
 Title: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved
     transcriptomics data
-Version: 1.13.5
-Date: 2023-09-05
+Version: 1.13.6
+Date: 2023-09-15
 Authors@R:
     c(
     person("Leonardo", "Collado-Torres", role = c("aut", "cre"), 

NEWS.md

@@ -1,3 +1,11 @@
+# spatialLIBD 1.13.6
+
+NEW FEATURES
+
+* `vis_clus_p()`, `vis_clus()`, and `vis_grid_clus()` now all use implement the
+`na_color` argument that was present in the `vis_gene()` functions. This
+resolves https://github.com/LieberInstitute/spatialLIBD/issues/43 by @boyiguo1.
+
 # spatialLIBD 1.13.5
 
 NEW FEATURES

R/vis_clus.R

@@ -24,6 +24,11 @@
 #' @param auto_crop A `logical(1)` indicating whether to automatically crop
 #' the image / plotting area, which is useful if the Visium capture area is
 #' not centered on the image and if the image is not a square.
+#' @param na_color A `character(1)` specifying a color for the NA values.
+#' If you set `alpha = NA` then it's best to set `na_color` to a color that has
+#' alpha blending already, which will make non-NA values pop up more and the NA
+#' values will show with a lighter color. This behavior is lost when `alpha` is
+#' set to a non-`NA` value.
 #' @param ... Passed to [paste0()][base::paste] for making the title of the
 #' plot following the `sampleid`.
 #'
@@ -74,6 +79,20 @@
 #'         spatial = FALSE
 #'     )
 #'     print(p3)
+#'
+#'     ## With some NA values
+#'     spe$tmp <- spe$layer_guess_reordered
+#'     spe$tmp[spe$sample_id == "151673"][seq_len(500)] <- NA
+#'     p4 <- vis_clus(
+#'         spe = spe,
+#'         clustervar = "tmp",
+#'         sampleid = "151673",
+#'         colors = libd_layer_colors,
+#'         na_color = "white",
+#'         ... = " LIBD Layers"
+#'     )
+#'     print(p4)
+#'
 #' }
 vis_clus <- function(spe,
     sampleid = unique(spe$sample_id)[1],
@@ -97,6 +116,7 @@ vis_clus <- function(spe,
     alpha = NA,
     point_size = 2,
     auto_crop = TRUE,
+    na_color = "#CCCCCC40",
     ...) {
     spe_sub <- spe[, spe$sample_id == sampleid]
     d <- as.data.frame(cbind(colData(spe_sub), SpatialExperiment::spatialCoords(spe_sub)), optional = TRUE)
@@ -112,6 +132,7 @@ vis_clus <- function(spe,
         image_id = image_id,
         alpha = alpha,
         point_size = point_size,
-        auto_crop = auto_crop
+        auto_crop = auto_crop,
+        na_color = na_color
     )
 }

R/vis_clus_p.R

@@ -52,7 +52,8 @@ vis_clus_p <-
     image_id = "lowres",
     alpha = NA,
     point_size = 2,
-    auto_crop = TRUE) {
+    auto_crop = TRUE,
+    na_color = "#CCCCCC40") {
         ## Some variables
         pxl_row_in_fullres <- pxl_col_in_fullres <- key <- NULL
         # stopifnot(all(c("pxl_col_in_fullres", "pxl_row_in_fullres", "key") %in% colnames(d)))
@@ -112,7 +113,7 @@ vis_clus_p <-
                 alpha = alpha
             ) +
             coord_fixed(expand = FALSE) +
-            scale_fill_manual(values = colors) +
+            scale_fill_manual(values = colors, na.value = na_color) +
             xlim(0, ncol(img)) +
             ylim(nrow(img), 0) +
             xlab("") + ylab("") +

R/vis_gene.R

@@ -23,11 +23,6 @@
 #' dependent on cell density.
 #' @param cont_colors A `character()` vector of colors that supersedes the
 #' `viridis` argument.
-#' @param na_color A `character(1)` specifying a color for the NA values.
-#' If you set `alpha = NA` then it's best to set `na_color` to a color that has
-#' alpha blending already, which will make non-NA values pop up more and the NA
-#' values will show with a lighter color. This behavior is lost when `alpha` is
-#' set to a non-`NA` value.
 #'
 #' @return A [ggplot2][ggplot2::ggplot] object.
 #' @export

R/vis_grid_clus.R

@@ -61,6 +61,7 @@ vis_grid_clus <-
     sample_order = unique(spe$sample_id),
     point_size = 2,
     auto_crop = TRUE,
+    na_color = "#CCCCCC40",
     ...) {
         stopifnot(all(sample_order %in% unique(spe$sample_id)))
 
@@ -79,6 +80,7 @@ vis_grid_clus <-
                     alpha = alpha,
                     point_size = point_size,
                     auto_crop = auto_crop,
+                    na_color = na_color,
                     ...
                 )
             })