draft of "use_geoms"

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SpatialData.plot
 Title: SpatialData visualization
 Depends: R (>= 4.4), SpatialData
-Version: 0.99.1
+Version: 0.99.101
 Description: Visualization suit for 'SpatialData' (R). Current functionality 
     includes handling of multiscale 'images', visualizing 'labels', 'points', 
     and 'shapes'. For the latter, POINT, POLYGON, and MULTIPOLYGON geometries 

NAMESPACE

@@ -1,6 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
+export(add_points)
+export(add_tx)
 export(plotSpatialData)
+export(viewShape)
 exportMethods(plotImage)
 exportMethods(plotLabel)
 exportMethods(plotPoint)

R/use_geoms.R

@@ -0,0 +1,67 @@
+# functions here emphasize use of the coordinate data
+
+# shape rendering support
+# could transition to S4 if needed
+
+.shapenames = function(sdobj) {
+ stopifnot(is(sdobj, "SpatialData"))
+ names(shapes(sdobj))
+}
+
+.shapes2sf = function(sdobj, elem) {
+ stopifnot(elem %in% .shapenames(sdobj))
+ sf::st_as_sf(SpatialData::data(SpatialData::shapes(sdobj)[[elem]]))
+}
+
+.pointnames = function(sdobj) {
+ stopifnot(is(sdobj, "SpatialData"))
+ names(points(sdobj))
+}
+
+.txdf = function(sdobj) {
+ stopifnot("transcripts" %in% .pointnames(sdobj))
+ as.data.frame(data(points(sdobj)$transcripts))
+}
+
+.pointdf = function(sdobj, elem) {
+ stopifnot(elem %in% .pointnames(sdobj))
+ as.data.frame(data(points(sdobj)[[elem]]))
+}
+
+.available_transcripts = function(sdobj) {   # maybe too specific?  'points'?
+ txdf = .txdf(sdobj)
+ as.character(unique(txdf$feature_name)) # valid?  feature_name comes back as *factor*
+}
+
+#' Use geom_sf to view a shapes component
+#' @import ggplot2
+#' @param sdobj SpatialData instance
+#' @param elem character(1) name of a shapes component of sdobj
+#' @export
+viewShape = function(sdobj, elem) {
+ thesf = .shapes2sf(sdobj, elem)
+ ggplot2::ggplot(thesf) + ggplot2::geom_sf()
+}
+
+#' Use geom_point to enhance a visualization with viewShape
+#' @param sdobj SpatialData instance
+#' @param featurename character(1) name of a shapes component of sdobj
+#' @param size numeric(1) target size for glyph
+#' @examples
+#' example(use_sdio) # produces br2fov
+#' viewShape(br2fov, "cell_boundaries") + add_tx(br2fov, "EPCAM")
+#' @export
+add_tx = function(sdobj, featurename, size=.1) {
+ txdf = .txdf(sdobj) |> dplyr::filter(feature_name == featurename)
+ ggplot2::geom_point(data=txdf, aes(x=x, y=y), size=size)
+}
+
+#' Use geom_point more generally than add_tx
+#' @param sdobj SpatialData instance
+#' @param featurename character(1) name of a shapes component of sdobj
+#' @param size numeric(1) target size for glyph
+#' @export
+add_points = function(sdobj, featurename, size=.1) {
+ pointdf = .pointdf(sdobj) 
+ ggplot2::geom_point(data=pointdf, aes(x=x, y=y), size=size)
+}

vignettes/use_geoms.Rmd

@@ -0,0 +1,102 @@
+---
+title: "`Some SpatialData visualizations based on ggplot2 for spatial features`"
+date: "`r format(Sys.Date(), '%B %d, %Y')`"
+package: "`r BiocStyle::pkg_ver('SpatialData')`"
+author:
+  - name: Helena Lucia Crowell
+  - name: Louise Deconinck
+  - name: Artür Manukyan
+  - name: Dario Righelli
+  - name: Estella Dong
+  - name: Vince Carey
+output:
+  BiocStyle::html_document
+vignette: |
+  %\VignetteIndexEntry{Some SpatialData visualizations}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+
+# Introduction
+
+In this vignette we explore how shape and point data in Xenium and
+MERFISH experiments can be visualized.  We use examples that
+can be retrieved from a Bioconductor bucket and cached in
+BiocFileCache, using utilities in SpatialData package.
+
+The xenium examples are:
+```{r lkx, message=FALSE}
+library(SpatialData)
+available_10x_xen_zips()
+```
+
+[1] "Xenium_V1_human_Breast_2fov_outs.zip"
+[2] "Xenium_V1_human_Lung_2fov_outs.zip"  
+
+
+# Breast sample, "two fields of view"
+
+## A view of "image data"
+
+```{r getbr, message=FALSE}
+pa <- path_to_10x_xen_demo("Xenium_V1_human_Breast_2fov_outs.zip")
+dir.create(td <- tempfile())
+unzip(pa, exdir=td)
+# read & write to .zarr w/ 'spatialdata-io'
+target <- tempfile()
+nn = use_sdio("xenium", srcdir=td, dest=target) # returns NULL
+# read into R
+(br2fov <- readSpatialData(target))
+library(SpatialData.plot)
+plotSpatialData() + plotImage(br2fov)
+```
+
+## A view of the segmentation
+
+```{r lkcb, message=FALSE}
+library(ggplot2)
+viewShape(br2fov, "cell_boundaries")
+```
+
+## Add points for a specific 'transcript'
+
+```{r lkcb2, message=FALSE}
+viewShape(br2fov, "cell_boundaries") + add_tx(br2fov, "EPCAM")
+unlink(target, recursive=TRUE)
+```
+
+# Lung sample, "two fields of view"
+
+## Image
+
+```{r getlu, message=FALSE}
+pa <- path_to_10x_xen_demo("Xenium_V1_human_Lung_2fov_outs.zip")
+dir.create(td <- tempfile())
+unzip(pa, exdir=td)
+target <- tempfile()
+nn = use_sdio("xenium", srcdir=td, dest=target) # returns NULL
+(lu2fov <- readSpatialData(target))
+plotSpatialData() + plotImage(lu2fov)
+```
+
+## Transcripts on segmentation
+
+```{r lklu2, message=FALSE}
+viewShape(lu2fov, "cell_boundaries") + add_tx(lu2fov, "EPCAM")
+```
+
+# MERFISH example
+
+In this demo, we show how to take advantage of
+size information in the shape data on cells.
+
+```{r lkmerf}
+tf = tempfile()
+dir.create(tf)
+pa = unzip_merfish_demo(tf)
+pa
+merf = readSpatialData(pa)
+merfs = SpatialData.plot:::.shapes2sf(merf, "cells")
+ggplot(merfs) + geom_sf(colour="gray", size=merfs$radius/20)
+```