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| # Advanced scRNA-seq Cheatsheet | ||
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| #### 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. | ||
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| ##### You may also be interested in the following additional cheatsheets: | ||
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| - Download the PDF for the [Introduction to R and Tidyverse cheatsheet](https://github.com/AlexsLemonade/training-modules/raw/master/module-cheatsheets/intro-to-R-tidyverse-cheatsheet.pdf) | ||
| - Download the PDF for the [Introduction to Single-Cell RNA sequencing cheatsheet](https://github.com/AlexsLemonade/training-modules/raw/master/module-cheatsheets/scRNA-seq-cheatsheet.pdf) | ||
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| > 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. | ||
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| <!-- 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** | ||
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| - [`scater`](#scater) | ||
| - [`miQC`](#miqc) | ||
| - [`batchelor` and `harmony`](#batchelor-and-harmony) | ||
| - [`pheatmap` and `EnhancedVolcano`](#pheatmap-and-enhancedvolcano) | ||
| - [`tidyverse` functions](#tidyverse-functions) | ||
| - [`purrr` functions](#purrr-functions) | ||
| - [`ggplot2` functions](#ggplot2-functions) | ||
| - [`dplyr`, `tidyr`,`stringr`, and `tibble` functions](#dplyr-tidyrstringr-and-tibble-functions) | ||
| - [`Seurat` and `SCE` object conversion](#seurat-and-sce-object-conversion) | ||
| - [Converting from `Seurat` to `SCE`](#converting-from-seurat-to-sce) | ||
| - [Converting from `SCE` to `Seurat`](#converting-from-sce-to-seurat) | ||
| <!-- END doctoc generated TOC please keep comment here to allow auto update --> | ||
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| <div style="page-break-after: always;"></div> | ||
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| ### `scater` | ||
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| Read the [`scater` package documentation](https://rdrr.io/bioc/scater/), and a [vignette on its usage](http://www.bioconductor.org/packages/release/bioc/vignettes/scater/inst/doc/overview.html). | ||
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| <br> | ||
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| | Library/Package | Piece of Code | What it's called | What it does | | ||
| |----------------------|----------------------------|--------------------------------------------|--------------------------------------------------------------| | ||
| | `scater`| [`plotReducedDim()`](https://rdrr.io/bioc/scater/man/plotReducedDim.html)| Plot reduced dimensions | Plot a given reduced dimension slot from a `SingleCellExperiment` object by its name | | ||
| | `scater`| [`plotUMAP()`](https://rdrr.io/bioc/scater/man/plot_reddim.html)| Plot UMAP | Plot the "UMAP"-named reduced dimension slot from a `SingleCellExperiment` object | | ||
| | `scater`| [`plotExpression()`](https://rdrr.io/bioc/scater/man/plotExpression.html)| Plot expression | Plot expression values for all cells in a `SingleCellExperiment` object, using the `logcounts` assay by default| | ||
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| ### `miQC` | ||
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| Read the [`miQC` package documentation](https://rdrr.io/github/greenelab/miQC/), and a [vignette on its usage](https://www.bioconductor.org/packages/release/bioc/vignettes/miQC/inst/doc/miQC.html). | ||
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| | Library/Package | Piece of Code | What it's called | What it does | | ||
| |----------------------|----------------------------|--------------------------------------------|--------------------------------------------------------------| | ||
| | `miQC`| [`mixtureModel()`](https://rdrr.io/github/greenelab/miQC/man/mixtureModel.html)| Mixture model | Fit a `miQC` mixture model to a `SingleCellExperiment` object for use in filtering | | ||
| | `miQC`| [`filterCells()`](https://rdrr.io/github/greenelab/miQC/man/filterCells.html)| Filter cells | Filter cells from a `SingleCellExperiment` object based on a `miQC` model, returning a filtered `SingleCellExperiment` object | | ||
| | `miQC`| [`plotMetrics()`](https://rdrr.io/github/greenelab/miQC/man/plotMetrics.html)| Plot metrics | Plot percent of mitochondrial reads against the number of unique genes found for each cell | | ||
| | `miQC`| [`plotModel()`](https://rdrr.io/github/greenelab/miQC/man/plotModel.html)| Plot model | `miQC::plotMetics()` with the `miQC` fitted model overlaid | | ||
| | `miQC`| [`plotFiltering()`](https://rdrr.io/github/greenelab/miQC/man/plotFiltering.html)| Plot filtering | Plot percent of mitochondrial reads against the number of unique genes found, coloring points based on whether they will be filtered out or not | | ||
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| ### `batchelor` and `harmony` | ||
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| Read the [`batchelor` package documentation](https://rdrr.io/cran/batchelor/), and a [vignette on its usage](https://rdrr.io/bioc/batchelor/f/vignettes/correction.Rmd). | ||
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| Read the [`harmony` package documentation](https://rdrr.io/github/immunogenomics/harmony/man/harmony.html), and a [vignette on its usage](https://cran.r-project.org/web/packages/harmony/vignettes/quickstart.html). | ||
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| | Library/Package | Piece of Code | What it's called | What it does | | ||
| |----------------------|----------------------------|--------------------------------------------|--------------------------------------------------------------| | ||
| | `batchelor`| [`MultiBatchPCA()`](https://rdrr.io/bioc/batchelor/man/multiBatchPCA.html)| Multi-batch PCA | Perform PCA across multiple gene expression matrices, weighted by batch size | | ||
| | `batchelor`| [`fastMNN()`](https://rdrr.io/bioc/batchelor/man/fastMNN.html)| Fast mutual nearest neighbors correction | Perform integration on an SCE object with mutual nearest neighbors using the `fastMNN` algorithm, returning an SCE object with batch-corrected principal components | | ||
| | `harmony`| [`HarmonyMatrix()`](https://rdrr.io/github/immunogenomics/harmony/man/HarmonyMatrix.html)| Perform `harmony` integration on a matrix | Perform integration with `harmony` on either a matrix of principle components or gene expression, returning a matrix of batch-corrected principal components | | ||
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| ### `pheatmap` and `EnhancedVolcano` | ||
| Read the [`pheatmap` package documentation](https://rdrr.io/cran/pheatmap/). | ||
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| Read the [`EnhancedVolcano` package documentation](https://rdrr.io/bioc/EnhancedVolcano/), and [vignette on its usage](https://bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html). | ||
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| | Library/Package | Piece of Code | What it's called | What it does | | ||
| |----------------------|----------------------------|--------------------------------------------|--------------------------------------------------------------| | ||
| | `pheatmap`| [`pheatmap()`](https://rdrr.io/cran/pheatmap/man/pheatmap.html)| Pretty heatmap | Plot a (pretty!) clustered heatmap | | ||
| | `EnhancedVolcano`| [`EnhancedVolcano()`](https://rdrr.io/bioc/EnhancedVolcano/man/EnhancedVolcano.html)| Enhanced volcano | Plot a volcano plot to visualize differential expression analysis results | | ||
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| ### `tidyverse` functions | ||
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| #### `purrr` functions | ||
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| Read the [`purrr` package documentation](https://purrr.tidyverse.org/) and a [vignette on its usage](https://purrr.tidyverse.org/articles/base.html), and download the [`purr` package cheatsheet](https://github.com/rstudio/cheatsheets/blob/main/purrr.pdf). | ||
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| | Library/Package| Piece of Code| What it's called| What it does | | ||
| |----------------|--------------|-----------------|--------------| | ||
| | `purrr`| [`map()`](https://purrr.tidyverse.org/reference/map.html)| map | Apply a function across each element of list; return a list | | ||
| | `purrr`| [`imap()`](https://purrr.tidyverse.org/reference/imap.html)| imap | Apply a function across each element of list and its index/names; return a list | | ||
| | `purrr`| [`map2()`](https://purrr.tidyverse.org/reference/map2.html)| map2 | Apply a function across each element of two lists at a time; return a list | | ||
| | `purrr`| [`reduce()`](https://purrr.tidyverse.org/reference/reduce.html)| Reduce | Reduce a list to a single value by applying a given function | | ||
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| Note that `purrr::map()` functions can take advantage of R's new (as of version 4.1.0) [anonymous function syntax](https://rdrr.io/r/base/function.html): | ||
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| ```r | ||
| # One-line syntax: | ||
| \(x) # function code goes here # | ||
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| # Multi-line syntax: | ||
| \(x) { | ||
| # function code goes # | ||
| # inside the curly braces # | ||
| } | ||
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| # Example: Use an anonymous function with `purrr::map()` | ||
| # to get the colData's rownames for each SCE in `list_of_sce_objects` | ||
| purrr::map( | ||
| list_of_sce_objects, | ||
| \(x) rownames(colData(x)) | ||
| ) | ||
| ``` | ||
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| #### `ggplot2` functions | ||
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| Read the [`ggplot2` package documentation](https://ggplot2.tidyverse.org/) and an [overall reference for `ggplot2` functions](https://ggplot2.tidyverse.org/reference/index.html), and download the [`ggplot2` package cheatsheet](https://github.com/rstudio/cheatsheets/blob/main/data-visualization.pdf). | ||
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| | Library/Package| Piece of Code| What it's called| What it does | | ||
| |----------------|--------------|-----------------|--------------| | ||
| | `ggplot2` | [`geom_bar()`](https://ggplot2.tidyverse.org/reference/geom_bar.html) | Barplot | Creates a barplot of counts for a given categorical variable when added as a layer to a `ggplot()` object | | ||
| | `ggplot2` | [`scale_fill_brewer()`](https://ggplot2.tidyverse.org/reference/scale_brewer.html) | Add brewer fill scale | Apply a Brewer "fill" color palette to a categorical variable in a `ggplot()` object | | ||
| | `ggplot2` | [`guides()`](https://ggplot2.tidyverse.org/reference/guides.html) | Guides | Function to customize legend ("guide") appearance | | ||
| | `ggplot2` | [`facet_grid()`](https://ggplot2.tidyverse.org/reference/facet_grid.html) | Facet grid | Plot individual panels using specified variables to subset the data across rows and/or columns of a grid | | ||
| | `ggplot2` | [`vars()`](https://ggplot2.tidyverse.org/reference/vars.html) | Vars | Helper function to specify variables to `facet_grid()` or `facet_wrap()`| | ||
| | `ggplot2` | [`theme_bw()`](https://ggplot2.tidyverse.org/reference/ggtheme.html) | Black and white theme | Display `ggplot` with gridlines but a white background | | ||
| | `ggplot2` | [`theme()`](https://ggplot2.tidyverse.org/reference/theme.html) | Theme | Customize elements of a `ggplot` plot theme | | ||
| | `ggplot2` | [`element_text()`](https://ggplot2.tidyverse.org/reference/element.html) | Element text | Customize textual elements of a `ggplot` theme | | ||
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| #### `dplyr`, `tidyr`,`stringr`, and `tibble` functions | ||
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| Read the full documentation and download cheatsheets (where available) for these `tidyverse` packages at the following links: | ||
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| - [`dplyr` documentation](https://dplyr.tidyverse.org/) and [`dplyr` cheatsheet](https://github.com/rstudio/cheatsheets/blob/main/data-transformation.pdf) | ||
| - [`tidyr` documentation](https://tidyr.tidyverse.org/) and [`tidyr` cheatsheet](https://github.com/rstudio/cheatsheets/blob/main/tidyr.pdf) | ||
| - [`stringr` documentation](https://stringr.tidyverse.org/) and [`stringr` cheatsheet](https://github.com/rstudio/cheatsheets/blob/main/strings.pdf) | ||
| - [`tibble` documentation](https://tibble.tidyverse.org/) | ||
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| <br> | ||
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| | Library/Package| Piece of Code| What it's called| What it does | | ||
| |----------------|--------------|-----------------|--------------| | ||
| | `dplyr`| [`pull()`](https://dplyr.tidyverse.org/reference/pull.html) | Pull | Extract a single column from a data frame into a stand-alone vector | | ||
| | `dplyr`| [`count()`](https://dplyr.tidyverse.org/reference/count.html) | Count | Count the number of observations in each group of a data frame | | ||
| | `dplyr`| [`left_join()`](https://dplyr.tidyverse.org/reference/left_join.html)| Left join | Joins two data frames together, retaining only rows present in the first ("left") argument to the function | | ||
| | `dplyr`| [`relocate()`](https://dplyr.tidyverse.org/reference/relocate.html) | Relocate | Change column order in a data frame by relocating one or more columns | | ||
| | `dplyr`| [`case_when()`](https://dplyr.tidyverse.org/reference/case_when.html) | Case when | Return a value based on a set of `TRUE`/`FALSE` comparisons; a vectorized `if-else` | | ||
| | `tidyr`| [`pivot_longer()`](https://tidyr.tidyverse.org/reference/pivot_longer.html) | Pivot longer | Convert a "wide" format data frame to a "long" format data frame | | ||
| | `tibble`| [`as_tibble()`](https://tibble.tidyverse.org/reference/as_tibble.html) | As tibble | Convert an object to a tibble | | ||
| | `stringr`| [`str_detect()`](https://stringr.tidyverse.org/reference/str_detect.html) | String detect | Returns `TRUE`/`FALSE` if a string contains a given substring| | ||
| | `stringr`| [`str_starts()`](https://stringr.tidyverse.org/reference/str_starts.html) | String starts | Returns `TRUE`/`FALSE` if a string starts with a given substring| | ||
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| ### `Seurat` and `SCE` object conversion | ||
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| #### Converting from `Seurat` to `SCE` | ||
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| #### Converting from `SCE` to `Seurat` |
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