---
title: "Overview"
author:
- name: William Hutchison
affiliation: WEHI - Walter and Eliza Hall Institute of Medical Research
email: hutchison.w@wehi.edu.au
- name: Stefano Mangiola
affiliation: WEHI - Walter and Eliza Hall Institute of Medical Research
package: tidySpatialExperiment
output:
BiocStyle::html_document
abstract: |
A brief overview of the tidySpatialExperiment package - demonstrating the SpatialExperiment-tibble abstraction, compatibility with the *tidyverse* ecosystem, compatibility with the *tidyomics* ecosystem and a few helpful utility functions.
vignette: |
%\VignetteIndexEntry{Overview}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
# Introduction
tidySpatialExperiment provides a bridge between the
[SpatialExperiment](https://github.com/drighelli/SpatialExperiment)
package and the [*tidyverse*](https://www.tidyverse.org) ecosystem. It
creates an invisible layer that allows you to interact with a
`SpatialExperiment` object as if it were a tibble; enabling the use of
functions from [dplyr](https://github.com/tidyverse/dplyr),
[tidyr](https://github.com/tidyverse/tidyr),
[ggplot2](https://github.com/tidyverse/ggplot2) and
[plotly](https://github.com/plotly/plotly.R). But, underneath, your data
remains a `SpatialExperiment` object.
tidySpatialExperiment also provides six additional utility functions.
## Resources
If you would like to learn more about tidySpatialExperiment and *tidyomics*, the following links are a good place to start:
- [The tidySpatialExperiment
website](http://william-hutchison.github.io/tidySpatialExperiment/)
- [The tidyomics website](https://github.com/tidyomics)
The *tidyomics* ecosystem also includes packages for:
- Working with genomic features:
- [plyranges](https://github.com/sa-lee/plyranges), for tidy
manipulation of genomic range data.
- [nullranges](https://github.com/nullranges/nullranges), for tidy
generation of genomic ranges representing the null hypothesis.
- [plyinteractions](https://github.com/tidyomics/plyinteractions),
for tidy manipulation of genomic interaction data.
- Working with transcriptomic features:
- [tidySummarizedExperiment](https://github.com/stemangiola/tidySummarizedExperiment),
for tidy manipulation of `SummarizedExperiment` objects.
- [tidySingleCellExperiment](https://github.com/stemangiola/tidySingleCellExperiment),
for tidy manipulation of `SingleCellExperiment` objects.
- [tidyseurat](https://github.com/stemangiola/tidyseurat), for
tidy manipulation of `Seurat` objects.
- [tidybulk](https://github.com/stemangiola/tidybulk), for bulk
RNA-seq analysis.
- Working with cytometry features:
- [tidytof](https://github.com/keyes-timothy/tidytof), for tidy
manipulation of high-dimensional cytometry data.
- And a few associated packages:
- [tidygate](https://github.com/stemangiola/tidygate), for manual
gating of points in space.
- [tidyheatmap](https://github.com/stemangiola/tidyHeatmap/), for
modular heatmap contruction.
## Functions and utilities
| Package | Functions available |
|-----------------------------------|-------------------------------------|
| `SpatialExperiment` | All |
| `dplyr` | `arrange`,`bind_rows`, `bind_cols`, `distinct`, `filter`, `group_by`, `summarise`, `select`, `mutate`, `rename`, `left_join`, `right_join`, `inner_join`, `slice`, `sample_n`, `sample_frac`, `count`, `add_count` |
| `tidyr` | `nest`, `unnest`, `unite`, `separate`, `extract`, `pivot_longer` |
| `ggplot2` | `ggplot` |
| `plotly` | `plot_ly` |
| Utility | Description |
|-----------------------------------|-------------------------------------|
| `as_tibble` | Convert cell data to a `tbl_df` |
| `join_features` | Append feature data to cell data |
| `aggregate_cells` | Aggregate cell-feature abundance into a pseudobulk `SummarizedExperiment` object |
| `rectangle` | Select cells in a rectangular region of space |
| `ellipse` | Select cells in an elliptical region of space |
| `gate` | Interactively or programmatically select cells in an arbitrary region of space |
## Installation
You can install the stable version of tidySpatialExperiment from
Bioconductor.
```{r, eval=FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tidySpatialExperiment")
```
Or, you can install the development version of tidySpatialExperiment
from GitHub.
```{r, eval=FALSE}
if (!requireNamespace("pak", quietly = TRUE))
install.packages("pak")
pak::pak("william-hutchison/tidySpatialExperiment")
```
## Load data
Here, we attach tidySpatialExperiment and an example `SpatialExperiment`
object.
```{r, message=FALSE, results=FALSE}
# Load example SpatialExperiment object
library(tidySpatialExperiment)
example(read10xVisium)
```
```{r, echo=FALSE}
# Remove unneeded second sample from demo data
spe <-
spe |>
filter(sample_id == "section1")
```
## SpatialExperiment-tibble abstraction
A `SpatialExperiment` object represents assay-feature values as rows and
cells as columns. Additional information about the cells is stored in the
`reducedDims`, `colData` and `spatialCoords` slots.
tidySpatialExperiment provides a SpatialExperiment-tibble abstraction,
representing cells as rows and cell data as columns, in accordance with the
tidy observation-variable convention. The cell data is made up of information stored in the `colData` and `spatialCoords` slots.
The default view is now of the SpatialExperiment-tibble abstraction.
```{r}
spe
```
But, our data maintains its status as a `SpatialExperiment` object.
Therefore, we have access to all `SpatialExperiment` functions.
```{r}
spe |>
colData() |>
head()
spe |>
spatialCoords() |>
head()
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 filter cells by a variable of interest.
```{r}
spe |>
filter(array_col < 5)
```
And `mutate` can be used to add new variables, or modify the value of an
existing variable.
```{r}
spe |>
mutate(in_region = c(in_tissue & array_row < 10))
```
## Tidy with tidyr
Most functions from tidyr are also available. Here, `nest()` is used to
group the data by `sample_id`, and `unnest()` is used to ungroup the data.
```{r}
# Nest the SpatialExperiment object by sample_id
spe_nested <-
spe |>
nest(data = -sample_id)
# View the nested SpatialExperiment object
spe_nested
# Unnest the nested SpatialExperiment objects
spe_nested |>
unnest(data)
```
## Plot with ggplot2
The `ggplot()` function can be used to create a plot directly from a
`SpatialExperiment` object. This example also demonstrates how tidy
operations can be combined to build up more complex analysis.
```{r}
spe |>
filter(sample_id == "section1" & in_tissue) |>
# Add a column with the sum of feature counts per cell
mutate(count_sum = purrr::map_int(.cell, ~
spe[, .x] |>
counts() |>
sum()
)) |>
# Plot with tidySpatialExperiment and ggplot2
ggplot(aes(x = reorder(.cell, count_sum), y = count_sum)) +
geom_point() +
coord_flip()
```
## Plot with plotly
The `plot_ly()` function can also be used to create a plot from a
`SpatialExperiment` object.
```{r, eval=FALSE, message=FALSE, warning=FALSE}
spe |>
filter(sample_id == "section1") |>
plot_ly(
x = ~ array_col,
y = ~ array_row,
color = ~ in_tissue,
type = "scatter"
)
```
# Utilities
## Append feature data to cell data
The *tidyomics* ecosystem places an emphasis on interacting with cell
data. To interact with feature data, the `join_features()` function can be
used to append assay-feature values to cell data.
```{r}
# Join feature data in wide format, preserving the SpatialExperiment object
spe |>
join_features(features = c("ENSMUSG00000025915", "ENSMUSG00000042501"), shape = "wide") |>
head()
# Join feature data in long format, discarding the SpatialExperiment object
spe |>
join_features(features = c("ENSMUSG00000025915", "ENSMUSG00000042501"), shape = "long") |>
head()
```
## Aggregate cells
Sometimes, it is necessary to aggregate the gene-transcript abundance
from a group of cells into a single value. For example, when comparing
groups of cells across different samples with fixed-effect models.
The `aggregate_cells()` function can be used to aggregate cells by a
specified variable and assay, returning a `SummarizedExperiment` object.
```{r}
spe |>
aggregate_cells(in_tissue, assays = "counts")
```
## Elliptical and rectangular region selection
The `ellipse()` and `rectangle()` functions can be used to select cells by
their position in space.
```{r}
spe |>
filter(sample_id == "section1") |>
mutate(in_ellipse = ellipse(array_col, array_row, c(20, 40), c(20, 20))) |>
ggplot(aes(x = array_col, y = array_row, colour = in_ellipse)) +
geom_point()
```
## Interactive gating
For the interactive selection of cells in space, tidySpatialExperiment experiment provides `gate()`. This function uses [tidygate](https://github.com/stemangiola/tidygate), shiny and plotly to launch an interactive plot overlaying cells in position with image data. Additional parameters can be used to specify point colour, shape, size and alpha, either with a column in the SpatialExperiment object or a constant value.
```{r, eval=FALSE}
spe_gated <-
spe |>
gate(colour = "in_tissue", alpha = 0.8)
```
```{r, echo=FALSE}
# Load pre-recorded brush path from data for example
data("demo_brush_data", package = "tidySpatialExperiment")
tidygate_env <<- rlang::env()
tidygate_env$gates <- demo_brush_data
spe_gated <-
spe |>
gate(programmatic_gates = tidygate_env$gates)
```
A record of which points appear in which gates is appended to the SpatialExperiment object in the `.gated` column. To select cells which appear within any gates, filter for non-NA values. To select cells which appear within a specific gate, string pattern matching can be used.
```{r}
# Select cells within any gate
spe_gated |>
filter(!is.na(.gated))
# Select cells within gate 2
spe_gated |>
filter(stringr::str_detect(.gated, "2"))
```
Details of the interactively drawn gates are saved to `tidygate_env$gates`. This variable is overwritten each time interactive gates are drawn, so save it right away if you would like to access it later.
```{r}
# Inspect previously drawn gates
tidygate_env$gates |>
head()
```
```{r, eval=FALSE}
# Save if needed
tidygate_env$gates |>
write_rds("important_gates.rds")
```
If previously drawn gates are supplied to the `programmatic_gates` argument, cells will be gated programmatically. This feature allows the reproduction of previously drawn interactive gates.
```{r, eval=FALSE}
important_gates <-
read_rds("important_gates.rds")
spe |>
gate(programmatic_gates = important_gates)) |>
filter(!is.na(.gated))
```
```{r, echo=FALSE}
spe |>
gate(programmatic_gates = tidygate_env$gates) |>
filter(!is.na(.gated))
```
# Special column behaviour
Removing the `.cell` column will return a tibble. This is consistent
with the behaviour in other *tidyomics* packages.
```{r}
spe |>
select(-.cell) |>
head()
```
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 |>
select(-sample_id)
# This change maintains separation of sample_ids and is permitted
spe |>
mutate(sample_id = stringr::str_c(sample_id, "_modified")) |>
head()
# This change does not maintain separation of sample_ids and produces an error
spe |>
mutate(sample_id = "new_sample")
```
The `pxl_col_in_fullres` and `px_row_in_fullres` columns cannot be
removed or modified with *tidyverse* functions. This is consistent with
the behaviour of dimension reduction data in other *tidyomics* packages.
```{r, error=TRUE}
# Attempting to remove pxl_col_in_fullres produces an error
spe |>
select(-pxl_col_in_fullres)
# Attempting to modify pxl_col_in_fullres produces an error
spe |>
mutate(pxl_col_in_fullres)
```
# Citation
If you use tidySpatialExperiment in published research, please cite [The tidyomics ecosystem: enhancing omic data analyses](https://doi.org/10.1038/s41592-024-02299-2).
# Session information
```{r}
sessionInfo()
```