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‎.gitignore

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inst/doc
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docs
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.Rhistory
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.Rbuildignore
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.Rproj*
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.Rproj.user

‎CODE_OF_CONDUCT.md

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# Contributor Covenant Code of Conduct
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## Our Pledge
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We as members, contributors, and leaders pledge to make participation in our
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community a harassment-free experience for everyone, regardless of age, body
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size, visible or invisible disability, ethnicity, sex characteristics, gender
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identity and expression, level of experience, education, socio-economic status,
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nationality, personal appearance, race, religion, or sexual identity and
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orientation.
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We pledge to act and interact in ways that contribute to an open, welcoming,
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diverse, inclusive, and healthy community.
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## Our Standards
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Examples of behavior that contributes to a positive environment for our
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community include:
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* Demonstrating empathy and kindness toward other people
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* Being respectful of differing opinions, viewpoints, and experiences
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* Giving and gracefully accepting constructive feedback
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* Accepting responsibility and apologizing to those affected by our mistakes,
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and learning from the experience
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* Focusing on what is best not just for us as individuals, but for the overall
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community
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Examples of unacceptable behavior include:
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* The use of sexualized language or imagery, and sexual attention or
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advances of any kind
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* Trolling, insulting or derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or email
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address, without their explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Enforcement Responsibilities
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Community leaders are responsible for clarifying and enforcing our standards
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of acceptable behavior and will take appropriate and fair corrective action in
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response to any behavior that they deem inappropriate, threatening, offensive,
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or harmful.
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Community leaders have the right and responsibility to remove, edit, or reject
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comments, commits, code, wiki edits, issues, and other contributions that are
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not aligned to this Code of Conduct, and will communicate reasons for moderation
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decisions when appropriate.
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## Scope
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This Code of Conduct applies within all community spaces, and also applies
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when an individual is officially representing the community in public spaces.
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Examples of representing our community include using an official e-mail
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address, posting via an official social media account, or acting as an appointed
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representative at an online or offline event.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported to the community leaders responsible for enforcement at [INSERT CONTACT
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METHOD]. All complaints will be reviewed and investigated promptly and fairly.
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All community leaders are obligated to respect the privacy and security of the
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reporter of any incident.
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## Enforcement Guidelines
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Community leaders will follow these Community Impact Guidelines in determining
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the consequences for any action they deem in violation of this Code of Conduct:
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### 1. Correction
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**Community Impact**: Use of inappropriate language or other behavior deemed
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unprofessional or unwelcome in the community.
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**Consequence**: A private, written warning from community leaders, providing
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clarity around the nature of the violation and an explanation of why the
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behavior was inappropriate. A public apology may be requested.
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### 2. Warning
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**Community Impact**: A violation through a single incident or series of
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actions.
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**Consequence**: A warning with consequences for continued behavior. No
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interaction with the people involved, including unsolicited interaction with
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those enforcing the Code of Conduct, for a specified period of time. This
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includes avoiding interactions in community spaces as well as external channels
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like social media. Violating these terms may lead to a temporary or permanent
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ban.
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### 3. Temporary Ban
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**Community Impact**: A serious violation of community standards, including
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sustained inappropriate behavior.
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**Consequence**: A temporary ban from any sort of interaction or public
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communication with the community for a specified period of time. No public or
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private interaction with the people involved, including unsolicited interaction
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with those enforcing the Code of Conduct, is allowed during this period.
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Violating these terms may lead to a permanent ban.
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### 4. Permanent Ban
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**Community Impact**: Demonstrating a pattern of violation of community
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standards, including sustained inappropriate behavior, harassment of an
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individual, or aggression toward or disparagement of classes of individuals.
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**Consequence**: A permanent ban from any sort of public interaction within the
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community.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage],
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version 2.0,
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available at https://www.contributor-covenant.org/version/2/0/
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code_of_conduct.html.
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Community Impact Guidelines were inspired by [Mozilla's code of conduct
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enforcement ladder](https://github.com/mozilla/diversity).
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[homepage]: https://www.contributor-covenant.org
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For answers to common questions about this code of conduct, see the FAQ at
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https://www.contributor-covenant.org/faq. Translations are available at https://
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www.contributor-covenant.org/translations.

‎DESCRIPTION

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Package: ggcoverage
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Type: Package
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Title: ggcoverage - Visualize genomic coverage with various annotaion.
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Version: 0.5.0
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Authors@R:
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person(given = "Yabing",
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family = "Song",
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role = c("aut", "cre"),
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email = "songyb0519@gmail.com")
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Maintainer: Yabing Song <songyb0519@gmail.com>
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Description: The goal of ggcoverage is to simplify the process of visualizing genomic coverage. It contains functions to
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load genomic data with bam/bigwig/bedgraph file format, create genomic coverage plot, add various annotation to
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the coverage plot, including gene annotaion, transcription annotion, ideogram annotation and peak annotation.
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License: MIT + file LICENSE
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 7.1.1
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Imports:
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biovizBase,
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dplyr,
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GenomicRanges,
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ggbio,
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ggh4x,
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ggplot2,
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ggrepel,
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grDevices,
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IRanges,
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magrittr,
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patchwork,
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RColorBrewer,
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rlang,
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Rsamtools,
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rtracklayer,
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scales,
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stats,
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utils
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Suggests:
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rmarkdown,
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knitr,
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BiocStyle,
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htmltools
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VignetteBuilder: knitr

‎LICENSE

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YEAR: 2022
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COPYRIGHT HOLDER: ggtrack authors

‎LICENSE.md

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# MIT License
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Copyright (c) 2022 ggcoverage authors
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎NAMESPACE

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# Generated by roxygen2: do not edit by hand
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S3method(ggplot_add,gene)
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S3method(ggplot_add,ideogram)
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S3method(ggplot_add,peak)
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S3method(ggplot_add,transcript)
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export(FormatTrack)
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export(LoadTrackFile)
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export(geom_coverage)
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export(geom_gene)
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export(geom_ideogram)
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export(geom_peak)
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export(geom_transcript)
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export(ggcoverage)
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export(theme_coverage)
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export(theme_coverage2)
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importFrom(GenomicRanges,GRanges)
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importFrom(GenomicRanges,makeGRangesFromDataFrame)
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importFrom(GenomicRanges,setdiff)
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importFrom(IRanges,IRanges)
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importFrom(IRanges,findOverlaps)
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importFrom(IRanges,subsetByOverlaps)
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importFrom(RColorBrewer,brewer.pal)
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importFrom(Rsamtools,indexBam)
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importFrom(biovizBase,getIdeogram)
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importFrom(dplyr,arrange)
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importFrom(dplyr,filter)
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importFrom(dplyr,group_by)
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importFrom(dplyr,select)
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importFrom(dplyr,summarise)
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importFrom(ggbio,layout_karyogram)
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importFrom(ggh4x,elem_list_rect)
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importFrom(ggh4x,facet_wrap2)
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importFrom(ggh4x,strip_themed)
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importFrom(ggplot2,aes)
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importFrom(ggplot2,aes_string)
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importFrom(ggplot2,annotate)
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importFrom(ggplot2,arrow)
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importFrom(ggplot2,coord_cartesian)
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importFrom(ggplot2,element_blank)
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importFrom(ggplot2,element_rect)
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importFrom(ggplot2,element_text)
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importFrom(ggplot2,expansion)
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importFrom(ggplot2,geom_polygon)
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importFrom(ggplot2,geom_rect)
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importFrom(ggplot2,geom_segment)
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importFrom(ggplot2,geom_text)
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importFrom(ggplot2,ggplot)
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importFrom(ggplot2,ggplot_add)
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importFrom(ggplot2,labs)
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importFrom(ggplot2,margin)
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importFrom(ggplot2,rel)
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importFrom(ggplot2,scale_color_manual)
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importFrom(ggplot2,scale_fill_manual)
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importFrom(ggplot2,scale_x_continuous)
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importFrom(ggplot2,scale_y_continuous)
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importFrom(ggplot2,theme)
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importFrom(ggplot2,theme_classic)
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importFrom(ggplot2,unit)
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importFrom(ggrepel,geom_text_repel)
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importFrom(grDevices,colorRampPalette)
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importFrom(magrittr,"%>%")
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importFrom(patchwork,wrap_plots)
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importFrom(rlang,.data)
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importFrom(rlang,as_label)
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importFrom(rtracklayer,import)
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importFrom(scales,comma)
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importFrom(stats,as.formula)
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importFrom(utils,read.csv)
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importFrom(utils,read.table)

‎NEWS.md

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# ggcoverage 0.5.0
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* First CRAN release.
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# ggcoverage 0.4.0
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## New features
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* Added `geom_peak` to enhance its usage in ChIP-seq or ATAC-seq data.
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* Change Y axis theme.
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-------------
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# ggcoverage 0.3.0
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## New features
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* Added `geom_transcript`, `geom_ideogram`.
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## Minor changes
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* Fix bug in `GetGeneGroup`.
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-------------
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# ggcoverage 0.2.0
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## New features
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* Added `geom_gene`, `geom_ideogram`.
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-------------
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# ggcoverage 0.1.0
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## New features
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* Added a `NEWS.md` file to track changes to the package.
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* Added `ggcoverage`, `geom_coverage`, `LoadTrack` and `FormatInput`.
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-------------

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