Merge pull request #792 from AlexsLemonade/jaclyn-taroni/782-pathway-…

…cheatsheet Update pathway analysis and RNA-seq cheatsheets
AlexsLemonade · Aug 8, 2024 · 2629aeb · 2629aeb
2 parents 155c784 + f26c610
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diff --git a/module-cheatsheets/RNA-seq-cheatsheet.md b/module-cheatsheets/RNA-seq-cheatsheet.md
@@ -18,7 +18,9 @@ If you have a different version of R or other R packages, the documentation may
 - [`FastQC` and `fastp`](#fastqc-and-fastp)
 - [`ggplot2`](#ggplot2)
 - [`tximeta` and `SummarizedExperiment`](#tximeta-and-summarizedexperiment)
-- [`stringr`, `readr`, `dplyr`, `pheatmap`](#stringr-readr-dplyr-pheatmap)
+- [`stringr`, `readr`, `dplyr`](#stringr-readr-dplyr)
+- [`ComplexHeatmap`](#complexheatmap)
+- [`matrixStats`](#matrixstats)
 - [Salmon](#salmon)
 
 <!-- END doctoc generated TOC please keep comment here to allow auto update -->
@@ -37,6 +39,7 @@ Read the [Base `R` package documentation](https://rdrr.io/r/).
 | Base `R`                | [`all.equal()`](https://rdrr.io/r/base/all.equal.html)               | All equal                 | Checks if two R objects are nearly equal                                 |
 | Base `R`                | [`attr()`](https://rdrr.io/r/base/attr.html)                         | Object Attributes         | Gets or sets the attributes of an object                                 |
 | Base `R`                | [`rowSums()`](https://rdrr.io/r/base/colSums.html)                   | Row Sums                  | Returns the sum of the rows in a numeric matrix-like object (i.e.. a matrix, data.frame, etc.) |
+| Base `R`                | [`rowMeans()`](https://rdrr.io/r/base/colSums.html)                  | Row Means                 | Returns the mean of the rows in a number matrix-like object (i.e.. a matrix, data.frame, etc.) |
 | Base `R`                | [`relevel()`](https://rdrr.io/r/stats/relevel.html)                  | Relevel                   | Reorders the levels of a factor as specified                             |
 | Base `R`                | [`summary()`](https://rdrr.io/r/base/summary.html)                   | Object Summary            | Returns a result summary of an object                                    |
 | Base `R`                | [`as.data.frame()`](https://rdrr.io/r/base/as.data.frame.html)       | Data Frame                | Checks if an object is a data.frame, and transforms the object into one, if possible |
@@ -98,7 +101,7 @@ Read the [`SummarizedExperiment` package documentation (PDF)](http://bioconducto
 | `SummarizedExperiment`| [`assay()`; `assayNames()`](https://rdrr.io/bioc/SummarizedExperiment/man/SummarizedExperiment-class.html)| Assay or Assay Names| Accesses the assay data or the names of the assays from `SummarizedExperiment` object|
 
 
-### `stringr`, `readr`, `dplyr`, `pheatmap`
+### `stringr`, `readr`, `dplyr`
 
 Documentation for each of these packages can be accessed by clicking the package name in the table below.
 
@@ -107,7 +110,25 @@ Documentation for each of these packages can be accessed by clicking the package
 | [`stringr`](https://stringr.tidyverse.org/index.html)            |[`word()`](https://stringr.tidyverse.org/reference/word.html)       | Word                            | Extracts words from a character vector                         |
 | [`readr`](https://readr.tidyverse.org/index.html)                 |[`write_rds()`](https://readr.tidyverse.org/reference/read_rds.html) | Write RDS                      | Writes data to a .RDS output file                                 |
 | [`dplyr`](https://dplyr.tidyverse.org/)                 | [`pull()`](https://dplyr.tidyverse.org/reference/pull.html)                      | Pull                              | Extracts a variable (column) as a vector                                          |
-| [`pheatmap`](https://rdrr.io/cran/pheatmap/)              | [`pheatmap()`](https://rdrr.io/cran/pheatmap/man/pheatmap.html)          | Pretty heatmap                          | Plots clustered heatmaps                                                 |
+
+### `ComplexHeatmap`
+
+Read the [`ComplexHeatmap` Complete Reference](https://jokergoo.github.io/ComplexHeatmap-reference/book/).
+
+| Library/Package               | Piece of Code                                                 | What it's called      | What it does                                                             |
+|-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------|
+| `ComplexHeatmap`              | [`Heatmap()`](https://rdrr.io/bioc/ComplexHeatmap/man/Heatmap.html) | Heatmap constructor | Constructs a `Heatmap` class object that can then be used to plot a heatmap    |
+| `ComplexHeatmap`              | [`HeatmapAnnotation()`](https://rdrr.io/bioc/ComplexHeatmap/man/HeatmapAnnotation.html) | Heatmap annotation constructor | Constructs a `HeatmapAnnotation` class object that can be used to annotate a heatmap |
+
+### `matrixStats`
+
+Read the [`matrixStats` package documentation (PDF)](https://cran.r-project.org/web/packages/matrixStats/matrixStats.pdf) and [summary of functions](https://cran.r-project.org/web/packages/matrixStats/vignettes/matrixStats-methods.html).
+
+| Library/Package               | Piece of Code                                                 | What it's called      | What it does                                                             |
+|-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------|
+| `matrixStats`                 | [`rowVars()`](https://www.rdocumentation.org/packages/matrixStats/versions/1.3.0/topics/rowVars) | Row variance                   | Estimates the variance for each row in a matrix |
+| `matrixStats`                 | [`rowSds()`](https://search.r-project.org/CRAN/refmans/matrixStats/html/rowSds.html) | Row standard deviations | Estimates the standard deviations for each row in a matrix |
+
 
 ### Salmon
 

diff --git a/module-cheatsheets/RNA-seq-cheatsheet.pdf b/module-cheatsheets/RNA-seq-cheatsheet.pdf
diff --git a/module-cheatsheets/pathway-analysis-cheatsheet.md b/module-cheatsheets/pathway-analysis-cheatsheet.md
@@ -16,7 +16,6 @@ If you have a different version of R or other R packages, the documentation may
 - [`msigdbr`](#msigdbr)
 - [AnnotationDbi](#annotationdbi)
 - [Base `R`](#base-r)
-- [`DESeq2`](#deseq2)
 - [`enrichplot`](#enrichplot)
 - [`clusterProfiler`](#clusterprofiler)
 - [`GSVA`](#gsva)
@@ -32,7 +31,7 @@ Read the [`msigdbr` documentation](https://rdrr.io/cran/msigdbr/f/README.md).
 
 | Library/Package| Piece of Code| What it's called| What it does |
 |----------------|--------------|-----------------|--------------|
-| `msigdbr`| [`msigdbr()`](https://rdrr.io/cran/msigdbr/man/msigdbr.html)| TODO | Retrieves the specified MSigDB dataset |
+| `msigdbr`| [`msigdbr()`](https://rdrr.io/cran/msigdbr/man/msigdbr.html)| Retrieve the MSigDB gene sets data frame | Retrieves the specified MSigDB dataset |
 
 ### AnnotationDbi
 
@@ -50,9 +49,11 @@ Read the [Base `R` documentation](https://rdrr.io/r/).
 |Library/Package|Piece of Code|What it's called| What it does|
 |---------------|-------------|----------------|-------------|
 | Base `R`| [`fisher.test()`](https://rdrr.io/r/stats/fisher.test.html)| Fisher's Exact Test | Performs the Fisher's exact test for testing the null of independence of rows and columns for a given matrix or data.frame with count data |
+| Base `R` | [`setdiff()`](https://rdrr.io/cran/probs/man/setdiff.html) | Set difference | Returns the difference of two sets (e.g., vectors) |
 
 <div style="page-break-after: always;"></div>
 
+<!--
 ### `DESeq2`
 
 Read the [`DESeq2` package documentation (PDF)](https://www.bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf), and the [package vignette by Love, Anders, and Huber](https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html).
@@ -63,6 +64,8 @@ Read the [`DESeq2` package documentation (PDF)](https://www.bioconductor.org/pac
 | `DESeq2`                | [`results()`](https://rdrr.io/bioc/DESeq2/man/results.html)             | Results                                         | Returns the results table from a DESeq2 analysis                         |
 | `DESeq2`                | [`resultsNames()`](https://rdrr.io/bioc/DESeq2/man/results.html)            | Results Names                                        | Returns the names of the estimated effects or coefficients of the `DESeq` model                         |
 
+-->
+
 ### `enrichplot`
 
 Read the [`enrichplot` package documentation (PDF)](https://bioconductor.org/packages/devel/bioc/manuals/enrichplot/man/enrichplot.pdf).
@@ -91,7 +94,7 @@ Read the [`GSVA` package documentation](https://www.bioconductor.org/packages/re
 | Library/Package               | Piece of Code                                                 | What it's called      | What it does                                                             |
 |-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------|
 | `GSVA`                | [`gsva()`](https://rdrr.io/github/rcastelo/GSVA/man/gsva.html)             | Gene Set Variation Analysis (GSVA)                                         | Estimates gene set variation analysis enrichment scores on given gene expression matrix                       |
-| `GSVA`                | [`gsvaParam()`](https://rdrr.io/github/rcastelo/GSVA/man/gsvaParam-class.html)             | Gene Set Variation Analysis (GSVA)                                         | Specify parameters to use with `gsva()`               |
+| `GSVA`                | [`gsvaParam()`](https://rdrr.io/github/rcastelo/GSVA/man/gsvaParam-class.html)             | Gene Set Variation Analysis (GSVA)  Parameters                                       | Specify parameters to use with `gsva()`               |
 
 
 ### `qusage`

diff --git a/module-cheatsheets/pathway-analysis-cheatsheet.pdf b/module-cheatsheets/pathway-analysis-cheatsheet.pdf