Update README

README.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "tidySpatialExperiment - part of tidytranscriptomics"
+title: "tidySpatialExperiment - part of tidyomics"
 output: github_document
 ---
 
@@ -11,7 +11,7 @@ output: github_document
 [![Lifecycle:experimental](https://img.shields.io/badge/lifecycle-experimental-blue.svg)](https://www.tidyverse.org/lifecycle/#experimental) [![R build status](https://github.com/william-hutchison/tidySpatialExperiment/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/william-hutchison/tidySpatialExperiment/actions)
 <!-- badges: end -->
 
-You can find more packages from the tidytranscriptomics ecosystem here:
+You can find more packages from the *tidyomics* ecosystem here:
 
 - [tidySingleCellExperiment](https://github.com/stemangiola/tidySingleCellExperiment) for tidy manipulation of SingleCellExperiment objects
 - [tidySummarizedExperiment](https://github.com/stemangiola/tidySummarizedExperiment) for tidy manipulation of SummarizedExperiment objects
@@ -58,7 +58,6 @@ install.packages("devtools")
 devtools::install_github("william-hutchison/tidySpatialExperiment")
 ```
 
-# Examples
 ## Load data
 
 Here, we load and view an example SpatialExperiment object. The output we see is of the SpatialExperiment-tibble abstraction.
@@ -69,6 +68,13 @@ library(tidySpatialExperiment)
 example(read10xVisium)
 ```
 
+```{r, echo=FALSE}
+# Load chromote for knitting
+library(chromote)
+```
+
+## View data
+
 ```{r}
 # View the SpatialExperiment-tibble abstraction
 spe
@@ -89,6 +95,7 @@ spe |>
   imgData()
 ```
 
+# Integration with the *tidyverse* ecosystem
 ## Manipulate with dplyr
 
 Most functions from *dplyr* are available for use with the SpatialExperiment-tibble abstraction. For example, `filter` can be used to select cells by a variable of interest. 
@@ -151,13 +158,48 @@ The `plot_ly` function can also be used to create a plot from a SpatialExperimen
 spe |>
   filter(sample_id == "section1") |>
   plot_ly(
-    x = ~ array_row, 
-    y = ~ array_col, 
+    x = ~ array_col, 
+    y = ~ array_row, 
     color = ~ in_tissue, 
     type = "scatter"
   )
 ```
 
+# Integration with the *tidyomics* ecosystem 
+
+## Interactively select cells with tidygate
+
+Different packages from the tidyomics ecosystem are easy to use together. Here, the tidygate package is used to interactively gate cells based on their array location.
+
+```{r, eval=FALSE}
+spe_regions <-
+  spe |> 
+  filter(sample_id == "section1") |>
+  mutate(region = tidygate::gate_chr(array_col, array_row))
+```
+
+![](README_files/tidygate_demo.gif)
+
+```{r, echo=FALSE}
+# Manually set gate information to match demonstration
+spe_regions <-
+  spe |> 
+  filter(sample_id == "section1") |>
+  mutate(region = ifelse(
+    array_row < 48 &
+    array_row > 20 &
+    array_col < 80 &
+    array_col > 60, 
+    1, 0))
+```
+The gated cells can then be divided into pseudobulks within a SummarizedExperiment object using tidySpatialExperiment's `aggregate_cells' utility function. 
+
+```{r}
+spe_regions_aggregated <-
+  spe_regions |>
+  aggregate_cells(region)
+```
+
 # Important considerations
 
 tidySpatialExperiment is still in development and contains some rough edges. Below are examples of behaviour that is currently unclear. I will be adding warning messages / making changes to address these problems in the coming weeks.
@@ -172,6 +214,7 @@ spe |>
 ```
 
 The sample_id column cannot be removed with tidyverse functions, and can only be modified if the changes are accepted by SpatialExperiment's `colData` function.
+
 ```{r, error=TRUE}
 # sample_id is not removed, despite the user's request
 spe |>

README.md

@@ -1,4 +1,4 @@
-tidySpatialExperiment - part of tidytranscriptomics
+tidySpatialExperiment - part of tidyomics
 ================
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
@@ -12,7 +12,7 @@ tidySpatialExperiment - part of tidytranscriptomics
 status](https://github.com/william-hutchison/tidySpatialExperiment/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/william-hutchison/tidySpatialExperiment/actions)
 <!-- badges: end -->
 
-You can find more packages from the tidytranscriptomics ecosystem here:
+You can find more packages from the *tidyomics* ecosystem here:
 
 - [tidySingleCellExperiment](https://github.com/stemangiola/tidySingleCellExperiment)
   for tidy manipulation of SingleCellExperiment objects
@@ -78,8 +78,6 @@ GitHub with:
     install.packages("devtools")
     devtools::install_github("william-hutchison/tidySpatialExperiment")
 
-# Examples
-
 ## Load data
 
 Here, we load and view an example SpatialExperiment object. The output
@@ -91,6 +89,8 @@ library(tidySpatialExperiment)
 example(read10xVisium)
 ```
 
+## View data
+
 ``` r
 # View the SpatialExperiment-tibble abstraction
 spe
@@ -157,6 +157,8 @@ spe |>
     ## 1    section1      lowres   ####   0.0510334
     ## 2    section2      lowres   ####   0.0510334
 
+# Integration with the *tidyverse* ecosystem
+
 ## Manipulate with dplyr
 
 Most functions from *dplyr* are available for use with the
@@ -274,7 +276,7 @@ spe |>
   ggplot2::coord_flip()
 ```
 
-![](README_files/figure-gfm/unnamed-chunk-7-1.png)<!-- -->
+![](README_files/figure-gfm/unnamed-chunk-8-1.png)<!-- -->
 
 ## Plot with plotly
 
@@ -285,14 +287,41 @@ SpatialExperiment object.
 spe |>
   filter(sample_id == "section1") |>
   plot_ly(
-    x = ~ array_row, 
-    y = ~ array_col, 
+    x = ~ array_col, 
+    y = ~ array_row, 
     color = ~ in_tissue, 
     type = "scatter"
   )
 ```
 
-![](README_files/figure-gfm/unnamed-chunk-8-1.png)<!-- -->
+![](README_files/figure-gfm/unnamed-chunk-9-1.png)<!-- -->
+
+# Integration with the *tidyomics* ecosystem
+
+## Interactively select cells with tidygate
+
+Different packages from the tidyomics ecosystem are easy to use
+together. Here, the tidygate package is used to interactively gate cells
+based on their array location.
+
+``` r
+spe_regions <-
+  spe |> 
+  filter(sample_id == "section1") |>
+  mutate(region = tidygate::gate_chr(array_col, array_row))
+```
+
+![](README_files/tidygate_demo.gif)
+
+The gated cells can then be divided into pseudobulks within a
+SummarizedExperiment object using tidySpatialExperiment’s
+\`aggregate_cells’ utility function.
+
+``` r
+spe_regions_aggregated <-
+  spe_regions |>
+  aggregate_cells(region)
+```
 
 # Important considerations