From ddf35bf22a31481a020abacf530b7f62bab3e225 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Tue, 28 May 2024 10:57:34 -0400
Subject: [PATCH] chore: update docs for `spatPlot2D()`

---
 R/vis_spatial.R | 19 ++++++++++++++-----
 man/spatPlot.Rd | 18 ++++++++++++++----
 2 files changed, 28 insertions(+), 9 deletions(-)

diff --git a/R/vis_spatial.R b/R/vis_spatial.R
index 16177af..a38e993 100644
--- a/R/vis_spatial.R
+++ b/R/vis_spatial.R
@@ -481,9 +481,6 @@
 #' @param theme_param list of additional params passed to `ggplot2::theme()`
 #' @details coord_fix_ratio: set to NULL to use default ggplot parameters
 #' @returns ggplot
-#' @examples
-#' g <- GiottoData::loadGiottoMini("visium")
-#' spatPlot2D(g)
 #' @export
 spatPlot2D <- function(
         gobject,
@@ -760,8 +757,20 @@ spatPlot2D <- function(
 #' @family spatial visualizations
 #' @returns ggplot
 #' @examples
-#' g <- GiottoData::loadGiottoMini("visium")
-#' spatPlot(g)
+#' g <- GiottoData::loadGiottoMini("visium", verbose = FALSE)
+#' spatPlot(g, show_image = TRUE, image_name = "image")
+#'
+#' # the more specific spatPlot2D with networks shown
+#' spatPlot2D(g, show_image = TRUE, image_name = "image", show_network = TRUE)
+#'
+#' # plotting of some cell metadata (number of different features detected)
+#' spatPlot2D(g,
+#'     show_image = TRUE,
+#'     image_name = "image",
+#'     cell_color = "nr_feats",
+#'     color_as_factor = FALSE,
+#'     gradient_style = "sequential"
+#' )
 #' @export
 #' @seealso \code{\link{spatPlot3D}}
 spatPlot <- function(...) {
diff --git a/man/spatPlot.Rd b/man/spatPlot.Rd
index 139ccbc..fc8b451 100644
--- a/man/spatPlot.Rd
+++ b/man/spatPlot.Rd
@@ -292,10 +292,20 @@ Visualize cells according to spatial coordinates
 coord_fix_ratio: set to NULL to use default ggplot parameters
 }
 \examples{
-g <- GiottoData::loadGiottoMini("visium")
-spatPlot2D(g)
-g <- GiottoData::loadGiottoMini("visium")
-spatPlot(g)
+g <- GiottoData::loadGiottoMini("visium", verbose = FALSE)
+spatPlot(g, show_image = TRUE, image_name = "image")
+
+# the more specific spatPlot2D with networks shown
+spatPlot2D(g, show_image = TRUE, image_name = "image", show_network = TRUE)
+
+# plotting of some cell metadata (number of different features detected)
+spatPlot2D(g,
+    show_image = TRUE,
+    image_name = "image",
+    cell_color = "nr_feats",
+    color_as_factor = FALSE,
+    gradient_style = "sequential"
+)
 }
 \seealso{
 \code{\link{spatPlot3D}}