feat: add spatial utilities for plotting in Seurat and Giotto

- Introduced a new R script `spatialutils.R` containing utility functions for spatial plotting.
- Defined arguments for spatial plot functions, including options for images, masks, shapes, and points.
- Implemented functions to handle background rectangles, extract points arguments, and process points layers for Seurat spatial plots.
- Added support for molecule-specific plotting and new scale layers.

Author: pwwang

R/spatialplot.R

@@ -62,6 +62,12 @@ $ conda install pwwang::r-scplotter
 
 ![](./man/figures/clonaldiv.png)
 
+## Spatial data
+
+[`SpatDimPlot`][23] | [`SpatFeaturePlot`][24]
+
+![](./man/figures/spatialplot.png)
+
 ## Visualization with LLMs
 
 ```r
@@ -107,3 +113,5 @@ chat$ask("Do a heatmap instead")
 [20]: https://pwwang.github.io/scplotter/reference/ClonalPositionalPlot.html
 [21]: https://github.com/ncborcherding/scRepertoire
 [22]: https://pwwang.github.io/scplotter/reference/ClonalDynamicsPlot.html
+[23]: https://pwwang.github.io/scplotter/reference/SpatDimPlot.html
+[24]: https://pwwang.github.io/scplotter/reference/SpatFeaturePlot.html

R/spatialutils.R

@@ -16,8 +16,22 @@ navbar:
         href: Seurat.10x_VisiumHD.html
       - text: "Visualizing SlideSeq data prepared with Seurat"
         href: Seurat.SlideSeq.html
+      - text: "Visualizing Xenium data prepared with Seurat"
+        href: Seurat.Xenium.html
+      - text: "Visualizing Nanostring CosMx data prepared with Seurat"
+        href: Seurat.Nanostring_CosMx.html
+      - text: "Visualizing Visium data prepared with Giotto"
+        href: Giotto.Visium.html
+      - text: "Visualizing VisiumHD data prepared with Giotto"
+        href: Giotto.VisiumHD.html
       - text: "Visualizing Xenium data prepared with Giotto"
-        href: Giotto.XeniumInsitu.html
+        href: Giotto.Xenium.html
+      - text: "Visualizing SlideSeq data prepared with Giotto"
+        href: Giotto.SlideSeq.html
+      - text: "Visualizing Spatial CITE-Seq data prepared with Giotto"
+        href: Giotto.Spatial_CITE-Seq.html
+      - text: "Visualizing Nanostirng CosMx data prepared with Giotto"
+        href: Giotto.Nanostring_CosMx.html
 reference:
   - title: scRNA-seq
     desc: Functions for plotting single cell RNA-seq data