Add spatial cheatsheet

module-cheatsheets/spatial-cheatsheet.md

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+# Spatial Transcriptomics Cheatsheet
+
+#### The tables below consist of valuable functions or commands that will help you through this module.
+##### Each table represents a different library/tool and its corresponding commands.
+> Please note that these tables are not intended to tell you all the information you need to know about each command.
+>
+> The hyperlinks found in each piece of code will take you to the documentation for further information on the usage of each command.
+> Please be aware that the documentation will generally provide information about the given function's most current version (or a recent version, depending on how often the documentation site is updated).
+This will usually (but not always!) match what you have installed on your machine.
+If you have a different version of R or other R packages, the documentation may differ from what you have installed.
+
+
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+**Table of Contents**
+
+- [`SpatialExperiment`](#spatialexperiment)
+- [`VisiumIO`](#visiumio)
+- [`ggspavis`](#ggspavis)
+- [`SpotSweeper`](#spotsweeper)
+- [`scuttle`](#scuttle)
+- [`patchwork`](#patchwork)
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+
+<div style="page-break-after: always;"></div>
+
+
+### `SpatialExperiment`
+
+
+Read the [`SpatialExperiment` package documentation (and e-book)](https://bioconductor.org/books/release/OSTA/) and a [vignette on its usage](https://www.bioconductor.org/packages/release/bioc/vignettes/SpatialExperiment/inst/doc/SpatialExperiment.html).
+
+`SpatialExperiment` objects are based on [`SingleCellExperiment` objects](https://bioconductor.org/books/release/OSCA/).
+There are many functions that are shared between the two, with equivalent usage.
+See [this `SingleCellExperiment` vignette](https://bioconductor.org/packages/release/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html) for example usage of shared functions.
+You can also refer to the Data Lab cheatsheets for our "Introduction to scRNA-seq" (`scRNA-seq-cheatsheet.pdf`) and "Advanced scRNA-seq" (`scRNA-seq-advanced-cheatsheet.pdf`) training modules.
+
+
+
+| Library/Package      | Piece of Code      | What it's called    | What it does  |
+|----------------------|----------------------------|--------------------------------------------|--------------------------------------------------------------|
+| `SpatialExperiment` | [`SpatialExperiment()`](https://www.bioconductor.org/packages/release/bioc/vignettes/SpatialExperiment/inst/doc/SpatialExperiment.html) | Spatial Experiment| Creates a `SpatialExperiment` object  |
+| `SpatialExperiment` | [`spatialCoords()`](https://www.bioconductor.org/packages/release/bioc/vignettes/SpatialExperiment/inst/doc/SpatialExperiment.html#13_spatialCoords) | Spatial Experiment coordinates | Extracts spatial coordinates of spots in the `SpatialExperiment` object  |
+| `SpatialExperiment` | [`imgData()`](https://www.bioconductor.org/packages/release/bioc/vignettes/SpatialExperiment/inst/doc/SpatialExperiment.html#14_imgData) | Spatial Experiment images | View the image data associated with a `SpatialExperiment` object   |
+
+
+
+
+### `VisiumIO`
+
+<!-- TODO: This package has not yet made it to rdrr -->
+Read the R package [`VisiumIO` documentation](https://www.bioconductor.org/packages/release/bioc/html/VisiumIO.html) and a [vignette on its usage](https://www.bioconductor.org/packages/release/bioc/vignettes/VisiumIO/inst/doc/VisiumIO.html).
+
+|Library/Package|Piece of Code|What it's called| What it does|
+|---------------|-------------|----------------|-------------|
+| `VisiumIO` | [`TENxVisium()`](https://www.bioconductor.org/packages/release/bioc/vignettes/VisiumIO/inst/doc/VisiumIO.html#tenxvisium) | 10x Visium | Constructor function for importing 10x Visium data |
+| `VisiumIO`| [`import()`](https://www.bioconductor.org/packages/release/bioc/vignettes/VisiumIO/inst/doc/VisiumIO.html#importing-into-spatialexperiment) | Import | Loads 10x Visium data defined with the `TENxVisium()` constructor function |
+
+
+
+
+### `ggspavis`
+
+<!-- TODO: This package has not yet made it to rdrr -->
+Read the [`ggspavis` package documentation](https://www.bioconductor.org/packages/release/bioc/html/ggspavis.html) and a [vignette on its usage](https://www.bioconductor.org/packages/release/bioc/vignettes/ggspavis/inst/doc/ggspavis_overview.html).
+
+
+
+| Library/Package      | Piece of Code      | What it's called    | What it does  |
+|----------------------|----------------------------|--------------------------------------------|--------------------------------------------------------------|
+| `ggspavis` | [`plotCoords()`](https://www.bioconductor.org/packages/release/bioc/vignettes/ggspavis/inst/doc/ggspavis_overview.html#spot-shape---slide-seq-and-visium) | Plot coordinates | Creates a spot plot showing spatial locations in x/y with options for spot annotation  |
+| `ggspavis` | [`plotVisium()`](https://www.bioconductor.org/packages/release/bioc/vignettes/ggspavis/inst/doc/ggspavis_overview.html#spot-shape---slide-seq-and-visium) | Plot Visium | Creates a spot plot for Visium data specifically showing spatial locations in x/y with options for spot annotation as well as an option to show the spatial image, e.g., the H&E image  |
+
+
+<div style="page-break-after: always;"></div>
+
+
+
+### `SpotSweeper`
+
+
+<!-- TODO: This package has not yet made it to rdrr -->
+Read the [`SpotSweeper` package documentation](https://www.bioconductor.org/packages/release/bioc/html/SpotSweeper.html) and a [vignette on its usage](https://www.bioconductor.org/packages/release/bioc/vignettes/SpotSweeper/inst/doc/getting_started.html).
+
+
+
+| Library/Package      | Piece of Code      | What it's called    | What it does  |
+|----------------------|----------------------------|--------------------------------------------|--------------------------------------------------------------|
+| `SpotSweeper` | [`localOutliers()`](https://www.bioconductor.org/packages/release/bioc/vignettes/SpotSweeper/inst/doc/getting_started.html#identifying-local-outliers-using-spotsweeper)  | Local outliers | Detect local outlier spots in a `SpatialExperiment` based on a given quality control metric |
+| `SpotSweeper`| [`plotQCmetrics()`](https://www.bioconductor.org/packages/release/bioc/vignettes/SpotSweeper/inst/doc/getting_started.html#visualizing-local-outliers)| Plot QC metrics | Create a spot plot highlighting outliers detected with `SpotSweeper::localOutliers()` |
+
+
+
+
+### `scuttle`
+
+
+Read the [`scuttle` package documentation](https://rdrr.io/bioc/scuttle/), and a [vignette on its usage](https://rdrr.io/bioc/scuttle/f/vignettes/overview.Rmd).
+
+
+| Library/Package      | Piece of Code      | What it's called    | What it does  |
+|----------------------|----------------------------|--------------------------------------------|--------------------------------------------------------------|
+| `scuttle` | [`computeLibraryFactors()`](https://rdrr.io/bioc/scuttle/man/librarySizeFactors.html)  | Compute Library Factors | Returns a numeric vector of computed size factors for each spot (or cell) stored in a `SpatialExperiment` (or `SingleCellExperiment`) object. The size factor is computed as the library size of each spot/cell after scaling them to have a mean of 1 across all spots/cells |
+| `scuttle`| [`logNormCounts()`](https://rdrr.io/bioc/scuttle/man/logNormCounts.html)| Normalize log counts | Returns the `SpatialExperiment` (or `SingleCellExperiment`) object with normalized expression values for each spot (cell), using the size factors stored in the object |
+
+
+### `patchwork`
+
+
+Read the [`patchwork` package documentation](https://rdrr.io/cran/patchwork), and a [vignette on its usage](https://patchwork.data-imaginist.com/articles/patchwork.html).
+
+
+| Library/Package      | Piece of Code      | What it's called    | What it does  |
+|----------------------|----------------------------|--------------------------------------------|--------------------------------------------------------------|
+| `patchwork` | [`wrap_plots()`](https://rdrr.io/cran/patchwork/man/wrap_plots.html)  | Wrap plots | Wrap multiple `ggplot2` objects into a single multi-panel plot  |
+| `patchwork` | [`+`](https://rdrr.io/cran/patchwork/man/wrap_plots.html)  | Plot arithmetic | Place `ggplot2` objects side-by-side by adding them together with a `+`. The `patchwork` package must be loaded to use this symbol with plots |
+| `patchwork` | [`/`](https://rdrr.io/cran/patchwork/man/wrap_plots.html)  | Plot arithmetic | Stack `ggplot2` objects on top of one another "dividing" them with a `/`. The `patchwork` package must be loaded to use this symbol with plots |