### Quick Start: Install and Analyze Immune Repertoire Data with immunarch in R

Source: https://github.com/immunomind/immunarch/blob/master/README.md

This R code snippet provides a quick start guide for using the `immunarch` package. It covers installing the package, loading a test dataset, and performing initial immune repertoire analyses such as computing and visualizing repertoire overlap, gene usage, and diversity, including grouping samples by metadata.

```R
install.packages("immunarch")           # Install the package
library(immunarch); data(immdata)       # Load the package and the test dataset
repOverlap(immdata$data) %>% vis()      # Compute and visualise the most important statistics:
geneUsage(immdata$data[[1]]) %>% vis()  #     public clonotypes, gene usage, sample diversity
repDiversity(immdata$data) %>% vis(.by = "Status", .meta = immdata$meta)      # Group samples
```

--------------------------------

### Install immunarch R Package from CRAN

Source: https://github.com/immunomind/immunarch/blob/master/README.md

Installs the latest stable release of the `immunarch` R package from CRAN, the official R package repository. This command is the simplest way to get started with `immunarch`.

```R
install.packages("immunarch")
```

--------------------------------

### Commit Naming Examples

Source: https://github.com/immunomind/immunarch/blob/master/CONTRIBUTION.md

Examples demonstrating the recommended format for commit messages, including type, scope, and message, with optional issue linking.

```Text
feat(diversity): added the Chao1 method for diversity estimations
```

```Text
fix(clonality): fixed a bug in clonality computations #12
```

--------------------------------

### Install immunarch R Package from GitHub (Latest Release)

Source: https://github.com/immunomind/immunarch/blob/master/README.md

Installs the latest stable release of the `immunarch` R package directly from its GitHub repository. This method requires the `devtools` and `pkgload` packages for installation and reloading.

```R
install.packages(c("devtools", "pkgload")) # skip this if you already installed these packages
devtools::install_github("immunomind/immunarch")
devtools::reload(pkgload::inst("immunarch"))
```

--------------------------------

### Install immunarch R Package from GitHub (Pre-release/Dev Branch)

Source: https://github.com/immunomind/immunarch/blob/master/README.md

Installs the latest pre-release version of the `immunarch` R package directly from the 'dev' branch on GitHub. This provides access to bleeding-edge features and optimisations not yet available on CRAN. Requires `devtools` and `pkgload`.

```R
install.packages(c("devtools", "pkgload")) # skip this if you already installed these packages
devtools::install_github("immunomind/immunarch", ref="dev")
devtools::reload(pkgload::inst("immunarch"))
```

--------------------------------

### Load immunarch Package and Test Data

Source: https://github.com/immunomind/immunarch/blob/master/README.md

Loads the `immunarch` R package into the environment and then loads its built-in test dataset (`immdata`) for immediate use in analyses.

```R
library(immunarch)  # Load the package into R
data(immdata)  # Load the test dataset
```

--------------------------------

### Calculate and Visualize Basic Immune Repertoire Statistics

Source: https://github.com/immunomind/immunarch/blob/master/README.md

Demonstrates how to calculate and visualize key statistics of immune repertoires. This includes visualizing the length distribution of CDR3 regions using `repExplore` and the relative abundance of clonotypes using `repClonality`.

```R
repExplore(immdata$data, "lens") %>% vis()  # Visualise the length distribution of CDR3
repClonality(immdata$data, "homeo") %>% vis()  # Visualise the relative abundance of clonotypes
```

--------------------------------

### Load Custom Immune Repertoire Data

Source: https://github.com/immunomind/immunarch/blob/master/README.md

Shows how to load custom immune repertoire data files into `immunarch`. The `repLoad` function automatically detects the file format, requiring only the path to your data.

```R
library(immunarch)  # Load the package into R
immdata <- repLoad("path/to/your/data")  # Replace it with the path to your data. Immunarch automatically detects the file format.
```

--------------------------------

### BibTex Citation for immunarch R Package

Source: https://github.com/immunomind/immunarch/blob/master/README.md

Provides the BibTex entry for citing the `immunarch` R package in academic publications, including author, title, publication year, DOI, and URL.

```BibTex
@misc{immunomind_team_2019_3367200,
  author       = {{ImmunoMind Team}},
  title        = {{immunarch: An R Package for Painless Bioinformatics Analysis 
                    of T-Cell and B-Cell Immune Repertoires}},
  month        = aug,
  year         = 2019,
  doi          = {10.5281/zenodo.3367200},
  url          = {https://doi.org/10.5281/zenodo.3367200}
}
```

--------------------------------

### immunarch 0.3.0: New File Format Support and Data Persistence

Source: https://github.com/immunomind/immunarch/blob/master/NEWS.md

Adds support for the AIRR file format and experimental support for the 10xGenomics format. Introduces `repSave` and `repLoad` functions for saving and loading data in `immunarch` and VDJtools formats.

```APIDOC
File Format Support:
  AIRR: Added support for AIRR file format.
  10xGenomics: Added experimental support for 10xGenomics format.

repSave, repLoad:
  Purpose: Save and load `immunarch` format data.
  Purpose: Save and load VDJtools format data.
```

--------------------------------

### Explore and Compare T-cell and B-cell Repertoires

Source: https://github.com/immunomind/immunarch/blob/master/README.md

Illustrates methods for comparing immune repertoires. This includes building heatmaps of public clonotypes shared between repertoires using `repOverlap`, visualizing V-gene distribution for a specific repertoire using `geneUsage`, and assessing repertoire diversity grouped by patient status using `repDiversity`.

```R
repOverlap(immdata$data) %>% vis()  # Build the heatmap of public clonotypes shared between repertoires
geneUsage(immdata$data[[1]]) %>% vis()  # Visualise the V-gene distribution for the first repertoire
repDiversity(immdata$data) %>% vis(.by = "Status", .meta = immdata$meta)  # Visualise the Chao1 diversity of repertoires, grouped by the patient status
```

--------------------------------

### immunarch 0.3.2: Dependency and Parser Fixes

Source: https://github.com/immunomind/immunarch/blob/master/NEWS.md

Removes MonetDBLite from dependencies due to its removal from CRAN and includes a bug fix for the MiXCR parser.

```APIDOC
MonetDBLite:
  Status: Removed from dependencies (due to CRAN removal).

MiXCR Parser:
  Fix: Corrected a bug.
```

--------------------------------

### immunarch 0.4.0: Data Loading and Exploration Updates

Source: https://github.com/immunomind/immunarch/blob/master/NEWS.md

Updates the MiXCR parser to support newer file formats and adds a `.clones` argument to `repExplore`. The `repLoad` function now consistently returns data frames sorted by the 'Clones' column.

```APIDOC
MiXCR Parser:
  Update: Supports files from May 2019 release.
  Enhancement: Added more MiXCR file variants parsing.

repExplore:
  .clones argument: Added.

repLoad:
  Behavior: Returns data frames sorted by "Clones" column.
```

--------------------------------

### immunarch 0.3.1: Statistical Tests and VDJtools Parsers

Source: https://github.com/immunomind/immunarch/blob/master/NEWS.md

Introduces support for statistical tests in boxplots and barplots via the `.test` argument and adds parsers for older VDJtools formats.

```APIDOC
Boxplots & Barplots:
  Feature: Support statistical tests via the `.test` argument.

VDJtools Parsers:
  Feature: Added parsers for old VDJtools formats.
```

--------------------------------

### immunarch 0.4.0: Sampling and Rarefaction Updates

Source: https://github.com/immunomind/immunarch/blob/master/NEWS.md

Consolidates all sampling, downsampling, and resampling procedures into a single function, `repSample`, and adds normalization capabilities to rarefaction analysis.

```APIDOC
prop_sample:
  Status: Completely removed.

repSample:
  Purpose: Consolidates all downsampling, resampling, and sampling procedures.

Rarefaction:
  Enhancement: Added normalisation option.
```

--------------------------------

### immunarch 0.4.0: Minor Updates and Deprecations

Source: https://github.com/immunomind/immunarch/blob/master/NEWS.md

Includes minor updates such as removing the 'wei' option from `geneUsage`, adding `ggseqlogo` as a dependency, and introducing a `.transpose` argument to `vis_heatmap`. It also sets a new default for `repOverlap`'s `.col` argument and addresses various warnings.

```APIDOC
geneUsage:
  "wei" option: Removed due to being useless.

Dependencies:
  ggseqlogo: New dependency added for seq-logo plots.

vis_heatmap:
  .transpose argument: Added.
  Warnings: "fill" aesthetics warnings removed.

repOverlap:
  .col default: Changed to "aa" for comfortable usage.

MiXCR Parsing:
  Warnings: "NAs introduced by coercion" warnings removed.

Function Names:
  Short function names: Removed.
```

--------------------------------

### immunarch 0.4.0: Clonotype Tracking and Visualizations

Source: https://github.com/immunomind/immunarch/blob/master/NEWS.md

Adds the core functionality for tracking clonotypes over time or across different conditions, complemented by specific visualization methods to represent these tracking results.

```APIDOC
trackClonotype:
  Purpose: Track clonotypes.
  Visualizations: Dedicated plotting functions available for tracking results.
```

--------------------------------

### immunarch 0.4.0: Bug Fixes for Core Functions

Source: https://github.com/immunomind/immunarch/blob/master/NEWS.md

Addresses critical bugs across various core functions including `geneUsage`, `repExplore`, `vis_heatmap`, `vis_bar`, `vis_box`, `repOverlap`, `repLoad`, and `repClonality`, ensuring correct data processing and visualization.

```APIDOC
geneUsage:
  Fix: Corrected issue where first two columns with gene usages were swapped.

repExplore:
  Fix: Resolved issue preventing function from working with a single repertoire.

vis_heatmap:
  Fix: Corrected issue preventing function from working with `geneUsage` output.

Morisita-Horn Index:
  Fix: Corrected a bug in computation.

vis_bar, vis_box:
  Fix: Resolved issue preventing functions from working with numeric grouping variables.

repOverlap:
  Fix: Resolved failures when working on data tables with 'morisita', 'public', 'overlap', 'jaccard', and 'tversky' metrics.

repLoad:
  Fix: Resolved failures when parsing MiXCR files with zero clonotypes.

Visualizations:
  Fix: Corrected a bug in incorrect grouping.

Clonal Homeostasis & Clonotype Tracking:
  Fix: Resolved issues when not working properly with filtered coding.

repClonality (D50, "top", "clonal.prop"):
  Fix: Corrected wrong values returned when input data frame is not sorted.
```

--------------------------------

### immunarch 0.4.3: Public Clonotype Analysis and Visualizations

Source: https://github.com/immunomind/immunarch/blob/master/NEWS.md

Introduces new functionalities for computing and visualizing public clonotypes across different groups and repertoires. This includes a dedicated function for statistical analysis and several visualization tools.

```APIDOC
pubRepStatistics:
  Purpose: Compute public clonotypes across groups and repertoires.

vis_public_frequencies:
  Purpose: Visualize public repertoire frequencies.

vis_public_clonotypes:
  Purpose: Visualize specific public clonotypes.

vis_upset:
  Purpose: Visualize public repertoire overlaps using UpSet plots.

Kmers:
  Purpose: Analysis and plots for kmer sequences, including seqlogo/textlogo visualizations.
```

--------------------------------

### immunarch 0.3.1: Bug Fixes for Visualizations and Gene Usage

Source: https://github.com/immunomind/immunarch/blob/master/NEWS.md

Addresses grouping issues in visualizations, fixes statistical tests from `ggpubr`, and resolves a bug in `geneUsage` when used with `.type="family"`.

```APIDOC
Visualizations:
  Fix: Corrected a grouping bug.

ggpubr:
  Fix: Corrected statistical tests.

geneUsage:
  Fix: Resolved issue when used with `.type="family"`.
```

--------------------------------

### immunarch 0.3.3: New Parsers and Coding Function Updates

Source: https://github.com/immunomind/immunarch/blob/master/NEWS.md

Introduces a new parser for ArcherDX files and updates the MiXCR parser to support the 'targetSequences' column format. The coding function family is also updated to work exclusively with CDR3 amino acid sequences.

```APIDOC
ArcherDX Parser:
  Feature: New parser added.

MiXCR Parser:
  Update: Works with "targetSequences" column format.

Coding Function Family:
  Update: Works with CDR3 amino acid sequences only.
```

--------------------------------

### immunarch 0.3.3: Minor Parser and Visualization Updates

Source: https://github.com/immunomind/immunarch/blob/master/NEWS.md

Includes minor updates to parsing functions, such as replacing unresolved genes with NAs in ImmunoSEQ files and ensuring filenames are parsed correctly. It also adds a color palette argument to `vis_heatmap2` and modifies the default grid setting for `vis_hist` in gene usage analysis.

```APIDOC
ImmunoSEQ Parser:
  Update: Replaces all "unresolved" genes with NAs.

vis_heatmap2:
  Argument: Added an argument for the color palette.

vis_hist:
  Default: `.grid=F` by default for gene usage analysis.

Parsing Functions:
  Fix: Do not remove strings after dots in filenames.

Post-parsing Processing:
  Update: Removes all characters except for amino acid alphabet, `*`, and `~` for compatibility.
```

--------------------------------

### immunarch 0.4.0: Performance and Overlap Function Enhancements

Source: https://github.com/immunomind/immunarch/blob/master/NEWS.md

Significantly improves the performance of Morisita-Horn index computation and introduces an incremental overlap function with downsampling options and associated visualizations. It also refines how `repOverlap` handles duplicate clonotypes and column detection.

```APIDOC
Morisita-Horn Index:
  Improvement: Up to 3 times faster computation.

inc_overlap:
  Purpose: Incremental overlap function.
  Availability: Accessible from `repOverlap`.
  Options: Supports downsampling.
  Visualizations: Dedicated plotting functions available.

repOverlap:
  .dup argument: Removed. All equal clonotypes are now always merged and their counts summed.
  .quant argument: Removed. The column is now automatically detected.
```

--------------------------------

### immunarch 0.3.0: Enhanced Visualization Control with fixVis

Source: https://github.com/immunomind/immunarch/blob/master/NEWS.md

Significantly enhances the `fixVis` function, allowing it to support various legend types (size, shape, color, fill, linetype), plot figures directly to R console/RStudio 'Plots' tab, and control the number of columns in legends.

```APIDOC
fixVis:
  Legend Support: Now supports size, shape, color, fill, linetype legends.
  Plotting Output: Can plot figures to R console / RStudio "Plots" tab.
  Legend Control: Supports setting the number of columns in legends.
```

--------------------------------

### immunarch 0.4.0: Visualization Function Enhancements

Source: https://github.com/immunomind/immunarch/blob/master/NEWS.md

Enhances `vis_hist` to allow adding custom ggplot2 layers and supports grouping when data is grouped and grid plotting is enabled. Also adds a `.target` argument to incremental overlap visualizations.

```APIDOC
vis_hist:
  .add.layer argument: Allows adding any additional ggplot2 layers to plots in the output grid.
  Grouping: Supports grouping if data is grouped and `.grid` is TRUE.

Incremental Overlap Visualizations:
  .target argument: Added for specific targeting in plots.
```

--------------------------------

### Commit Types Specification

Source: https://github.com/immunomind/immunarch/blob/master/CONTRIBUTION.md

Defines the allowed types for commit messages, indicating the nature of the change.

```APIDOC
Commit Types:
  chore: Routine tasks, maintenance
  docs: Documentation updates
  feat: New feature implementation
  fix: Bug fix
  refactor: Code refactoring without new features or bug fixes
  test: Adding or modifying tests
  perf: Performance improvements
  style: Code style changes (formatting, semicolons, etc.)
```

--------------------------------

### Commit Scopes Specification

Source: https://github.com/immunomind/immunarch/blob/master/CONTRIBUTION.md

Defines the allowed scopes for commit messages, indicating the area of the codebase affected by the change.

```APIDOC
Commit Scopes:
  diversity: Changes in analysis/visualisation functions related to diversity
  overlap: Changes in analysis/visualisation functions related to overlap
  pub-rep: Changes in analysis/visualisation functions related to public repertoire
  clonality: Changes in analysis/visualisation functions related to clonality
  gene-usage: Changes in analysis/visualisation functions related to gene usage
  explore: Changes in analysis/visualisation functions related to exploration
  kmers: Changes in analysis/visualisation functions related to kmers
  spectratype: Changes in analysis/visualisation functions related to spectratype
  dynamics: Changes in analysis/visualisation functions related to dynamics
  tools: Changes in analysis/visualisation functions related to tools
  single-cell: Changes in analysis/visualisation functions related to single-cell
  vis: General changes in visualisation functions
  io: Changes in parsing functions
  db: Changes in databases support
  utility: Changes in additional functions (e.g., general statistics)
  data: Changes in data
  upkeep: Changes in NAMESPACE, DESCRIPTION, citations, ISSUE_TEMPLATE.md, etc. (excluding README)
  vignette: Changes in README and vignettes
  ci: Changes in Continuous Integration
  shiny: Changes in Shiny applications
```

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