ggmsa

https://github.com/yulab-smu/ggmsa
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ggmsa is an R package designed for the visualization and annotation of multiple sequence alignments,...
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### Install ggmsa from Bioconductor

Source: https://github.com/yulab-smu/ggmsa/blob/devel/README.md

This code snippet demonstrates how to install the ggmsa package from Bioconductor. It first checks if BiocManager is installed and installs it if necessary, then proceeds to install ggmsa.

```R
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("ggmsa")
```

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

### Install ggmsa Development Version from GitHub

Source: https://github.com/yulab-smu/ggmsa/blob/devel/README.md

This code snippet shows how to install the development version of the ggmsa package directly from GitHub using the devtools package. It first ensures devtools is installed and then uses install_github to fetch the latest version.

```R
if (!requireNamespace("devtools", quietly=TRUE))
    install.packages("devtools")
devtools::install_github("YuLab-SMU/ggmsa")
```

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

### Visualize Multiple Sequence Alignment with ggmsa

Source: https://github.com/yulab-smu/ggmsa/blob/devel/README.md

This example demonstrates a basic usage of the ggmsa package in R. It loads the library, specifies a protein sequence file, and then visualizes a portion of the alignment (from residue 221 to 280) with sequence logos and a bar plot, customizing character width and showing sequence names.

```R
library(ggmsa)
protein_sequences <- system.file("extdata", "sample.fasta", package = "ggmsa")
ggmsa(protein_sequences, start = 221, end = 280, char_width = 0.5, seq_name = TRUE) + geom_seqlogo() + geom_msaBar()
```

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

### ggmsa() examples with dontrun

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

This change involves wrapping examples for the `ggmsa()` function within `\dontrun{}`, which prevents these examples from being executed during package checks, often done for examples that might be slow or require specific data.

```R
\dontrun{ggmsa()}
```

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

### Fix partitioning error for sequence start > 1

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Resolves a partitioning error that occurred when the sequence starting point was greater than 1, ensuring correct data segmentation.

```R
# Bugfix: partitioning error when the sequence starting point greater than 1.
```

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

### Add available_colors(), available_fonts(), available_msa()

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces utility functions `available_colors()`, `available_fonts()`, and `available_msa()` to list the available color schemes, fonts, and MSA formats supported by the package.

```R
available_colors()
available_fonts()
available_msa()
```

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

### Support linking ggtreeExtra

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Enables ggmsa to work seamlessly with `ggtreeExtra`, allowing for integrated visualization of phylogenetic trees and sequence alignments.

```R
# supports linking ggtreeExtra.
```

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

### Add ggSeqBundle() for Sequence Bundles

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces `ggSeqBundle()` for plotting Sequence Bundles for MSAs, based on `ggolot2`. This provides a novel way to visualize relationships and patterns within sequence sets.

```R
ggSeqBundle()
```

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

### Add Hydrophobicity color scheme and border parameter

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces a new color scheme named `Hydrophobicity` and a `border` parameter, enhancing the ability to visualize sequence properties.

```R
ggmsa(..., color_scheme = "Hydrophobicity", border = TRUE)
```

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

### Import seqmagick for FASTA parsing

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Imports the `seqmagick` package to enable parsing of FASTA files, a common format for storing biological sequences.

```R
import(seqmagick)
```

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

### ggmsa package preparation for Bioconductor submission

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

This section details preparatory steps for submitting the ggmsa package to Bioconductor, including updating DESCRIPTION and NEWS files, adding documentation, cleaning code, and managing vignettes.

```R
# Prepare for submission to Bioconductor
```

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

### Use proportional scaling algorithm

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Adopts a proportional scaling algorithm, likely for rendering sequence elements or spacing, aiming for more accurate visual representation.

```R
# used a proportional scaling algorithm
```

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

### Customize colors with custom_color

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Adds support for customizing colors using the `custom_color` parameter, allowing users to define their own color palettes for MSA visualizations.

```R
ggmsa(..., custom_color = ...)
```

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

### Add consensus views

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces new consensus views for MSA visualization, providing different ways to represent the consensus sequence or patterns.

```R
# added consensus views
```

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

### Migrate sequence recombination functionality from seqcombo

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Integrates sequence recombination functionality from the `seqcombo` package into ggmsa, expanding its capabilities for analyzing sequence evolution.

```R
# Migration of sequence recombination functionality from seqcombo package.
```

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

### ggmaf visualization of genome alignment

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Adds a new function, `ggmaf`, for visualizing genome alignments. This feature expands ggmsa's capabilities to include genomic data visualization.

```R
ggmaf()
```

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

### Support plot sequence logo

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Adds support for plotting sequence logos, a common visualization method for MSAs that depicts sequence conservation.

```R
ggmsa(..., plot_type = "logo")
```

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

### Typo fix: posHighligthed to position_highlight

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Corrects a typo in the parameter name from `posHighligthed` (camelCase) to `position_highlight` (snake_case), improving code consistency and readability.

```R
ggmsa(..., position_highlight = ...)
```

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

### Add ggmotif() for plotting sequence motifs

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces `ggmotif()`, a function for plotting sequence motifs independently, allowing for focused analysis of conserved patterns.

```R
ggmotif()
```

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

### Add gghelix() and geom_helix()

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces new functions `gghelix()` and `geom_helix()` for visualizing helical structures or patterns within sequences, adding a new dimension to MSA visualization.

```R
gghelix()
geom_helix()
```

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

### Add posHighlighted parameter in ggmsa()

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Adds the `posHighlighted` parameter to `ggmsa()`, enabling users to highlight specific positions within the sequences.

```R
ggmsa(..., posHighlighted = c(10, 20))
```

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

### Add ignore_gaps parameter in consensus views

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces the `ignore_gaps` parameter for consensus views, allowing users to choose whether to include or exclude gaps when calculating consensus.

```R
ggmsa(..., consensus_view = TRUE, ignore_gaps = TRUE)
```

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

### Add Monospaced Font DroidSansMono

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Includes the `DroidSansMono` font, providing a monospaced font option for displaying sequences in a consistent and readable manner.

```R
ggmsa(..., font = "DroidSansMono")
```

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

### Add facet_msa() function for MSA faceting

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces a new function `facet_msa()` designed to break down and display multiple sequence alignments in separate panels (facets), facilitating comparative analysis.

```R
facet_msa()
```

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

### tidy_msa for converting MSA to tidy data frame

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces `tidy_msa` functionality for converting MSA files or objects into a tidy data frame format, facilitating easier data manipulation and analysis.

```R
tidy_msa(msa_object)
```

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

### Add by_conservation view

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces a new visualization view called `by_conservation`, likely displaying sequence conservation information directly within the alignment plot.

```R
ggmsa(..., view = "by_conservation")
```

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

### Debug tree + geom_facet(geom_msa())

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Addresses a debugging issue where `tree + geom_facet(geom_msa())` was not functioning correctly, ensuring proper integration of trees and faceted alignments.

```R
# Debug: tree + geom_facet(geom_msa()) does not work.
```

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

### Fix assignment error in seqlogo.R

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Resolves an assignment error occurring on line 155 of the `seqlogo.R` file, ensuring the correct functionality of sequence logo generation.

```R
# Fixed assignment error on line 155 'seqlogo.R'
```

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

### Add geom_seqlogo() for plotting sequence motifs

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces `geom_seqlogo()`, a function for plotting sequence logos, which visually represent the conservation and frequency of nucleotides or amino acids at each position in an MSA.

```R
geom_seqlogo()
```

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

### Add geom_seed() for highlighting seed regions

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces a new function `geom_seed()` specifically designed to highlight seed regions within miRNA sequences in an MSA.

```R
geom_seed()
```

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

### Initial CRAN release

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Marks the initial release of the ggmsa package to the Comprehensive R Archive Network (CRAN), making it publicly available for R users.

```R
# initial CRAN release
```

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

### Add internal outline polygons

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces internal outline polygons, potentially for highlighting specific regions or boundaries within the sequence alignment visualization.

```R
# added internal outline polygons
```

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

### Add LETTER and CN6 colors

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Incorporates new color palettes named `LETTER` and `CN6`, provided by ShixiangWang, expanding the available color options for MSA visualization.

```R
ggmsa(..., color_scheme = "LETTER")
ggmsa(..., color_scheme = "CN6")
```

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

### Create geom_asterisk() layer

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces a new layer `geom_asterisk()` as an optimization for `geom_seed()`, likely used for marking specific points or regions in the alignment.

```R
geom_asterisk()
```

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

### Generate continuous x-axis labels for each panel

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Fixes an issue where continuous x-axis labels were not generated correctly for each panel in faceted plots, improving axis readability.

```R
# Bugfix: generates continuous x-axis labels for each panel.
```

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

### Import R4RNA to fix R check

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Imports the `R4RNA` package to resolve issues identified during R package checks, ensuring better compatibility and stability.

```R
import(R4RNA)
```

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

### Option to show fill legend

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Adds an option to display the fill legend in plots, allowing users to better understand the mapping of colors to data values.

```R
ggmsa(..., show_fill_legend = TRUE)
```

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

### Rewrite facet_msa() function

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Refactors the `facet_msa()` function, likely improving its performance, flexibility, or fixing underlying bugs related to faceting alignments.

```R
facet_msa()
```

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

### Add geom_GC() for plotting GC content

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces `geom_GC()`, a function designed to visualize the GC content of sequences within an MSA.

```R
geom_GC()
```

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

### Debug consensus views

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Fixes bugs identified in the consensus views functionality, ensuring accurate and reliable display of consensus information.

```R
# debug in consensus views
```

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

### Fix variable names error in color_scheme

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Corrects an error related to variable names within the `color_scheme` functionality, ensuring accurate color mapping and application.

```R
# Bugfix: fix variable names error in color_scheme.
```

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

### Add geom_msaBar() function

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces a new function `geom_msaBar()` for creating bar plots within MSA visualizations, potentially for representing scores, frequencies, or other quantitative data.

```R
geom_msaBar()
```

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

### Fix warning message in msa_data.R

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Resolves a warning message generated within the `msa_data.R` file, improving the robustness of data handling.

```R
# fixed warning message in msa_data.R
```

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

### Add three fonts: helvetical, times_new_roman, mono

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Includes three new font options: `helvetical`, `times_new_roman`, and `mono`, providing users with more choices for text rendering in plots.

```R
ggmsa(..., font = "helvetical")
ggmsa(..., font = "times_new_roman")
ggmsa(..., font = "mono")
```

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

### Add error message for unique sequence names

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Implements an error message to remind users that sequences must have unique names, preventing potential issues arising from duplicate identifiers.

```R
# Added an error message to remind that "sequences must have unique names".
```

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

### Replace geom_xspline with ggfun::geom_xspline

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

This update replaces the usage of `ggalt::geom_xspline()` with `ggfun::geom_xspline()`, indicating a shift in dependency or an improvement in the geom's implementation.

```R
ggalt::geom_xspline() # Replaced with
ggfun::geom_xspline()
```

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

### Add seq_name parameter in ggmsa()

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces the `seq_name` parameter to the `ggmsa()` function, allowing users to specify or control sequence names in the plot.

```R
ggmsa(..., seq_name = "Sequence1")
```

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

### Add ggplot_add methods for geom_*()

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Implements `ggplot_add` methods for `geom_*` functions, enabling seamless integration of ggmsa geoms into ggplot2 plots.

```R
ggplot() + geom_msa()
```

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

### treeMSA_plot ancestral sequence selection

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Introduces a new feature for the `treeMSA_plot` function that allows users to select ancestral sequences directly on the Tree-MSA plot, enhancing the analysis of evolutionary relationships.

```R
treeMSA_plot(..., select_ancestral = TRUE)
```

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

### Fix tidy_msa bug

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Corrects a bug within the `tidy_msa` function, ensuring that MSA data is correctly converted into a tidy data frame format.

```R
# bug fixed of tidy_msa
```

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

### Update default color schemes in SeqDiff plot

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Updates the default color schemes used in the lower part of the SeqDiff plot, potentially improving the visual distinction and interpretation of sequence differences.

```R
# update default color schemes in lower part of the SeqDiff plot
```

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

### Fix reversed sequence in tree + geom_facet(font)

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Corrects a bug where sequences were reversed when using `tree + geom_facet(font)`, ensuring correct orientation in combined plots.

```R
# Bugfix: reversed sequence in 'tree + geom_facet(font)' .
```

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

### Smoothed curve on simplot

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Enhances the `simplot` functionality by adding a smoothed curve, likely for better trend visualization or noise reduction in similarity plots.

```R
simplot(..., smooth = TRUE)
```

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

### geom_msaBar conservation layer alignment fix

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Addresses an issue where the conservation layer in `geom_msaBar` was incorrectly aligned. This bugfix ensures proper visual representation of conservation information in MSA bar plots.

```R
# Bugfix: geom_msaBar conservation layer incorrectly aligned issues#34
```

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

### Fix logical OR operator usage

Source: https://github.com/yulab-smu/ggmsa/blob/devel/NEWS.md

Corrects an error where the logical OR operator `||` was used instead of the bitwise OR operator `|` on line 110 in `geom_msa.R`, likely affecting conditional logic.

```R
# Fixed error: using || instead of | on 110 lines in geom_msa.R
```
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