diff --git a/index.html b/index.html
index 6a1d61e..4bbc317 100644
--- a/index.html
+++ b/index.html
@@ -50,7 +50,7 @@
-The MolEvolvR R-package provides a framework for characterizing proteins using molecular evolution and phylogeny. Check out our packagedown page here: jravilab.github.io/molevolvR
+The MolEvolvR R-package provides a framework for characterizing proteins using molecular evolution and phylogeny. Check out our pkgdown page here: jravilab.github.io/MolEvolvR
Installation
@@ -62,7 +62,7 @@
+BiocManager :: install ( "JRaviLab/MolEvolvR" )
Loading the package
diff --git a/pkgdown.yml b/pkgdown.yml
index 434c9e5..89934b6 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 3.1.11
pkgdown: 2.1.0
pkgdown_sha: ~
articles: {}
-last_built: 2024-09-12T19:32Z
+last_built: 2024-09-12T19:49Z
urls:
reference: https://jravilab.github.io/MolEvolvR/reference
article: https://jravilab.github.io/MolEvolvR/articles
diff --git a/reference/count_to_sunburst.html b/reference/count_to_sunburst.html
index d8487a8..c591bf6 100644
--- a/reference/count_to_sunburst.html
+++ b/reference/count_to_sunburst.html
@@ -90,21 +90,21 @@
On this page
diff --git a/search.json b/search.json
index 292b327..ac5cb42 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement codeofconduct@posit.co. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired [Mozilla’s code conduct enforcement ladder][https://github.com/mozilla/inclusion]. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contributing to MolEvolvR","title":"Contributing to MolEvolvR","text":"outlines propose change MolEvolvR. detailed discussion contributing tidyverse packages, please see development contributing guide code review principles.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"Contributing to MolEvolvR","text":"can fix typos, spelling mistakes, grammatical errors documentation directly using GitHub web interface, long changes made source file. generally means ’ll need edit roxygen2 comments .R, .Rd file. can find .R file generates .Rd reading comment first line.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":"bigger-changes","dir":"","previous_headings":"","what":"Bigger changes","title":"Contributing to MolEvolvR","text":"want make bigger change, ’s good idea first file issue make sure someone team agrees ’s needed. ’ve found bug, please file issue illustrates bug minimal reprex (also help write unit test, needed). See guide create great issue advice.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"Bigger changes","what":"Pull request process","title":"Contributing to MolEvolvR","text":"Fork package clone onto computer. haven’t done , recommend using usethis::create_from_github(\"JRaviLab/MolEvolvR\", fork = TRUE). Install development dependencies devtools::install_dev_deps(), make sure package passes R CMD check running devtools::check(). R CMD check doesn’t pass cleanly, ’s good idea ask help continuing. Create Git branch pull request (PR). recommend using usethis::pr_init(\"brief-description--change\"). Make changes, commit git, create PR running usethis::pr_push(), following prompts browser. title PR briefly describe change. body PR contain Fixes #issue-number. user-facing changes, add bullet top NEWS.md (.e. just first header). Follow style described https://style.tidyverse.org/news.html.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":"code-style","dir":"","previous_headings":"Bigger changes","what":"Code style","title":"Contributing to MolEvolvR","text":"New code follow tidyverse style guide. can use styler package apply styles, please don’t restyle code nothing PR. Lint Code: Ensure code adheres style guidelines using lintr: lintr::lint(\"path///file.R\") use roxygen2, Markdown syntax, documentation. use testthat unit tests. Contributions test cases included easier accept.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contributing to MolEvolvR","text":"Please note MolEvolvR project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"BSD 3-clause License","title":"BSD 3-clause License","text":"Copyright (c) 2024 MolEvolvR authors rights reserved. Redistribution use source binary forms, without modification, permitted provided following conditions met: Redistributions source code must retain copyright notice, list conditions following disclaimer. Redistributions binary form must reproduce copyright notice, list conditions following disclaimer documentation /materials provided distribution. Neither name copyright holder names contributors may used endorse promote products derived software without specific prior written permission. SOFTWARE PROVIDED COPYRIGHT HOLDERS CONTRIBUTORS “” EXPRESS IMPLIED WARRANTIES, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE DISCLAIMED. EVENT SHALL COPYRIGHT HOLDER CONTRIBUTORS LIABLE DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, CONSEQUENTIAL DAMAGES (INCLUDING, LIMITED , PROCUREMENT SUBSTITUTE GOODS SERVICES; LOSS USE, DATA, PROFITS; BUSINESS INTERRUPTION) HOWEVER CAUSED THEORY LIABILITY, WHETHER CONTRACT, STRICT LIABILITY, TORT (INCLUDING NEGLIGENCE OTHERWISE) ARISING WAY USE SOFTWARE, EVEN ADVISED POSSIBILITY DAMAGE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Janani Ravi. Author, maintainer. David Mayer. Author. Evan Brenner. Author. Faisal Alquaddoomi. Author. Samuel Chen. Contributor. Lo Sosinski. Contributor. Joseph Burke. Contributor. Jacob Krol. Contributor.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Ravi J, Mayer D, Brenner E, Alquaddoomi F (2024). MolEvolvR: Molecular Evolution Phylogeny. R package version 0.99.9, https://jravilab.github.io/MolEvolvR/, https://github.com/jravilab/molevolvr.","code":"@Manual{, title = {MolEvolvR: Molecular Evolution and Phylogeny}, author = {Janani Ravi and David Mayer and Evan Brenner and Faisal Alquaddoomi}, year = {2024}, note = {R package version 0.99.9, https://jravilab.github.io/MolEvolvR/}, url = {https://github.com/jravilab/molevolvr}, }"},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"molevolvr-","dir":"","previous_headings":"","what":"Molecular Evolution and Phylogeny","title":"Molecular Evolution and Phylogeny","text":"MolEvolvR R-package provides framework characterizing proteins using molecular evolution phylogeny. Check packagedown page : jravilab.github.io/molevolvR","code":""},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Molecular Evolution and Phylogeny","text":"can install development version MolEvolvR GitHub :","code":"# Install Bioconductor if (!require(\"BiocManager\", quietly = TRUE)) install.packages(\"BiocManager\") BiocManager::install(version = \"3.19\") # Install Development Version of molevolvR BiocManager::install(\"JRaviLab/MolEvolvR\", auth_token = '')"},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"loading-the-package","dir":"","previous_headings":"Installation","what":"Loading the package","title":"Molecular Evolution and Phylogeny","text":"","code":"library(molevolvR)"},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"Molecular Evolution and Phylogeny","text":"basic example shows analyze favorite protein:","code":"library(molevolvR) ## basic example code ## TBA"},{"path":[]},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"related-molevolvr-codebases","dir":"","previous_headings":"Companion repos & projects","what":"Related MolEvolvR codebases","title":"Molecular Evolution and Phylogeny","text":"MolEvolvR web-app 1.0 | 🔒Repo | Live web-app | Preprint | Case studies MolEvolvR web-app 2.0 | 🔒Repo","code":""},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"specific-use-cases","dir":"","previous_headings":"Companion repos & projects","what":"Specific use cases","title":"Molecular Evolution and Phylogeny","text":"PSP evolution across tree life | 🔒Repo | Live web-app | PubMed Bacterial phage defense system, avcDI | Repo | PubMed DciA evolution across bacteria | Repo | PubMed Internalins Listeria | Repo | PubMed","code":""},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"current-contributors","dir":"","previous_headings":"","what":"Current contributors","title":"Molecular Evolution and Phylogeny","text":"David Mayer | R-package, back-end Faisal Alquaddoomi | Front-end 1.0, back-end Evan Brenner | MolEvolvR functionality Vince Rubinetti | Front-end 2.0 Dave Bunten | Data management, engineering Janani Ravi | PI","code":""},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"contribution-guidelines","dir":"","previous_headings":"Current contributors","what":"Contribution guidelines","title":"Molecular Evolution and Phylogeny","text":"welcome contributions community! ensure smooth collaborative process, please follow guidelines 📜 License","code":""},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"code-of-conduct","dir":"","previous_headings":"Current contributors","what":"Code of Conduct","title":"Molecular Evolution and Phylogeny","text":"Please note MolEvolvR project released Contributor Code Conduct. contributing project, agree abide terms. ⏳ Stay tuned!","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/BinaryDomainNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Domain Network — BinaryDomainNetwork","title":"Domain Network — BinaryDomainNetwork","text":"function creates domain network 'DomArch' column. Domains part 'domains_of_interest' different node color domains. network domains returned based shared domain architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/BinaryDomainNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Domain Network — BinaryDomainNetwork","text":"","code":"BinaryDomainNetwork( prot, column = \"DomArch\", domains_of_interest, cutoff = 70, layout = \"nice\", query_color = adjustcolor(\"yellow\", alpha.f = 0.5), partner_color = adjustcolor(\"skyblue\", alpha.f = 0.5), border_color = adjustcolor(\"grey\", alpha.f = 0.8), IsDirected = T )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/BinaryDomainNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Domain Network — BinaryDomainNetwork","text":"prot data frame contains column 'DomArch'. column Name column containing Domain architecture nodes edges generated. cutoff Integer. use domains occur cutoff total counts cutoff_type \"Total Count\". use domains appear cutoff greater lineages cutoff_type Lineage. layout Character. Layout type used network. Options : \"circle\" \"random\" \"auto\" query_color Color nodes domains domains_of_interest vector colored partner_color Color nodes part domains_of_interest vector colored IsDirected network directed? Set false eliminate arrows","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/BinaryDomainNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Domain Network — BinaryDomainNetwork","text":"","code":"if (FALSE) { # \\dontrun{ domain_network(pspa) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/DownloadAssemblySummary.html","id":null,"dir":"Reference","previous_headings":"","what":"Download the combined assembly summaries of genbank and refseq — DownloadAssemblySummary","title":"Download the combined assembly summaries of genbank and refseq — DownloadAssemblySummary","text":"Download combined assembly summaries genbank refseq","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/DownloadAssemblySummary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download the combined assembly summaries of genbank and refseq — DownloadAssemblySummary","text":"","code":"DownloadAssemblySummary( outpath, keep = c(\"assembly_accession\", \"taxid\", \"species_taxid\", \"organism_name\") )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/DownloadAssemblySummary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download the combined assembly summaries of genbank and refseq — DownloadAssemblySummary","text":"outpath String path assembly summary file written keep Character vector containing columns retained downloaded","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/DownloadAssemblySummary.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Download the combined assembly summaries of genbank and refseq — DownloadAssemblySummary","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2lin.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2lin","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2lin","text":"Function map GCA_ID TaxID, TaxID Lineage","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2lin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2lin","text":"","code":"GCA2lin( prot_data, assembly_path = \"/data/research/jravilab/common_data/assembly_summary_genbank.txt\", lineagelookup_path = \"/data/research/jravilab/common_data/lineage_lookup.tsv\", acc_col = \"AccNum\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2lin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2lin","text":"prot_data Dataframe containing column GCA_ID assembly_path String path assembly_summary path file can generated using \"DownloadAssemblySummary()\" function lineagelookup_path String path lineage lookup file (taxid lineage mapping). file can generated using \"create_lineage_lookup()\" function acc_col","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2lin.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2lin","text":"Currently configured kingdom phylum","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2lin.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2lin","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GenContextNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Genomic Context Directed Network — GenContextNetwork","title":"Genomic Context Directed Network — GenContextNetwork","text":"function creates Genomic Context network 'GenContext' column. network Genomic Context returned.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GenContextNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Genomic Context Directed Network — GenContextNetwork","text":"","code":"GenContextNetwork( prot, domains_of_interest, column = \"GenContext\", cutoff = 40, layout = \"grid\", directed = TRUE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/GenContextNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Genomic Context Directed Network — GenContextNetwork","text":"prot data frame contains column 'GenContext'. domains_of_interest Character vector domains interest. column Name column containing Genomic Context nodes edges generated. cutoff Integer. use GenContexts occur cutoff percentage total count layout Character. Layout type used network. Options : \"circle\" \"random\" \"auto\" \"nice\" directed network directed?","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GenContextNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Genomic Context Directed Network — GenContextNetwork","text":"","code":"if (FALSE) { # \\dontrun{ gc_directed_network(pspa, column = \"GenContex\", cutoff = 55) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/LineagePlot.html","id":null,"dir":"Reference","previous_headings":"","what":"LineagePlot — LineagePlot","title":"LineagePlot — LineagePlot","text":"Generate lineage plot","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/LineagePlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"LineagePlot — LineagePlot","text":"","code":"LineagePlot(prot, domains_of_interest, level = 3, label.size = 8)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/LineagePlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"LineagePlot — LineagePlot","text":"prot Data frame containing DomArch Lineage Columns domains_of_interest Vector domains check presence lineages level max depth Lineage. ie) = Kingdom, 2 = Phylum, 3 = class ... label.size Size text labels","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/LineagePlot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"LineagePlot — LineagePlot","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/LineagePlot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"LineagePlot — LineagePlot","text":"","code":"if (FALSE) { # \\dontrun{ LineagePlot(psp_data, c( \"PspA\", \"Snf7\", \"Classical-AAA\", \"PspF\", \"PspB\", \"PspC\", \"ClgR\", \"PspM\", \"Thioredoxin\", \"PspN_N\", \"DUF3046\", \"LiaI-LiaF-TM\", \"Toast_rack\", \"REC\", \"HISKIN\", \"HAAS\", \"SHOCT-bihelical\", \"SHOCT-like\", \"Tfu_1009\", \"PspAA\", \"Spermine_synth\", \"TM-Flotillin\", \"Band-7\", \"Betapropeller\", \"MacB_PCD\", \"FTSW_RODA_SPOVE\", \"Cest_Tir\", \"SIGMA-HTH\", \"GNTR-HTH\", \"DUF2089-HTH\", \"PadR-HTH\", \"RHH\", \"ZnR\" ), level = 2 ) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/RepresentativeAccNums.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to generate a vector of one Accession number per distinct observation from 'reduced' column — RepresentativeAccNums","title":"Function to generate a vector of one Accession number per distinct observation from 'reduced' column — RepresentativeAccNums","text":"Function generate vector one Accession number per distinct observation 'reduced' column","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/RepresentativeAccNums.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to generate a vector of one Accession number per distinct observation from 'reduced' column — RepresentativeAccNums","text":"","code":"RepresentativeAccNums(prot_data, reduced = \"Lineage\", accnum_col = \"AccNum\") RepresentativeAccNums(prot_data, reduced = \"Lineage\", accnum_col = \"AccNum\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/RepresentativeAccNums.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to generate a vector of one Accession number per distinct observation from 'reduced' column — RepresentativeAccNums","text":"prot_data Data frame containing Accession Numbers reduced Column prot_data distinct observations generated . One accession number assigned observations accnum_col Column prot_data contains Accession Numbers","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/RepresentativeAccNums.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Function to generate a vector of one Accession number per distinct observation from 'reduced' column — RepresentativeAccNums","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2fa.html","id":null,"dir":"Reference","previous_headings":"","what":"acc2fa converts protein accession numbers to a fasta format. — acc2fa","title":"acc2fa converts protein accession numbers to a fasta format. — acc2fa","text":"Resulting fasta file written outpath. acc2fa converts protein accession numbers fasta format. Resulting fasta file written outpath.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2fa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"acc2fa converts protein accession numbers to a fasta format. — acc2fa","text":"","code":"acc2fa(accessions, outpath, plan = \"sequential\") acc2fa(accessions, outpath, plan = \"sequential\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2fa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"acc2fa converts protein accession numbers to a fasta format. — acc2fa","text":"accessions Character vector containing protein accession numbers generate fasta sequences . Function may work vectors length > 10,000 outpath str. Location fasta file written . plan","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2fa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"acc2fa converts protein accession numbers to a fasta format. — acc2fa","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2fa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"acc2fa converts protein accession numbers to a fasta format. — acc2fa","text":"","code":"if (FALSE) { # \\dontrun{ acc2fa(accessions = c(\"ACU53894.1\", \"APJ14606.1\", \"ABK37082.1\"), outpath = \"my_proteins.fasta\") Entrez:accessions <- rep(\"ANY95992.1\", 201) |> acc2fa(outpath = \"entrez.fa\") EBI:accessions <- c(\"P12345\", \"Q9UHC1\", \"O15530\", \"Q14624\", \"P0DTD1\") |> acc2fa(outpath = \"ebi.fa\") } # } if (FALSE) { # \\dontrun{ acc2fa(accessions = c(\"ACU53894.1\", \"APJ14606.1\", \"ABK37082.1\"), outpath = \"my_proteins.fasta\") Entrez:accessions <- rep(\"ANY95992.1\", 201) |> acc2fa(outpath = \"entrez.fa\") EBI:accessions <- c(\"P12345\", \"Q9UHC1\", \"O15530\", \"Q14624\", \"P0DTD1\") |> acc2fa(outpath = \"ebi.fa\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2lin.html","id":null,"dir":"Reference","previous_headings":"","what":"acc2lin — acc2lin","title":"acc2lin — acc2lin","text":"function combines 'efetch_ipg()' 'ipg2lin()' map set protein accessions assembly (GCA_ID), tax ID, lineage. Function map protein accession numbers lineage function combines 'efetch_ipg()' 'ipg2lin()' map set protein accessions assembly (GCA_ID), tax ID, lineage.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2lin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"acc2lin — acc2lin","text":"","code":"acc2lin( accessions, assembly_path, lineagelookup_path, ipgout_path = NULL, plan = \"multicore\" ) acc2lin( accessions, assembly_path, lineagelookup_path, ipgout_path = NULL, plan = \"multicore\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2lin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"acc2lin — acc2lin","text":"accessions Character vector protein accessions assembly_path String path assembly_summary path file can generated using \"DownloadAssemblySummary()\" function lineagelookup_path String path lineage lookup file (taxid lineage mapping). file can generated using ipgout_path Path write results efetch run accessions ipg database. NULL, file written. Defaults NULL plan","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2lin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"acc2lin — acc2lin","text":"Describe return, detail","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2lin.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"acc2lin — acc2lin","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2lin.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"acc2lin — acc2lin","text":"","code":"if (FALSE) { # \\dontrun{ acc2lin() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_leaves.html","id":null,"dir":"Reference","previous_headings":"","what":"Adding Leaves to an alignment file w/ accessions — add_leaves","title":"Adding Leaves to an alignment file w/ accessions — add_leaves","text":"Adding Leaves alignment file w/ accessions Genomic Contexts vs Domain Architectures. Adding Leaves alignment file w/ accessions Genomic Contexts vs Domain Architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_leaves.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adding Leaves to an alignment file w/ accessions — add_leaves","text":"","code":"add_leaves( aln_file = \"\", lin_file = \"data/rawdata_tsv/all_semiclean.txt\", reduced = FALSE ) add_leaves( aln_file = \"\", lin_file = \"data/rawdata_tsv/all_semiclean.txt\", reduced = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_leaves.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Adding Leaves to an alignment file w/ accessions — add_leaves","text":"aln_file Character. Path file. Input tab-delimited file + alignment file accnum & alignment. Default 'pspa_snf7.aln' lin_file Character. Path file. Protein file accession + number lineage mapping. Default 'pspa.txt' reduced Boolean. TRUE, reduced data frame generated one sequence per lineage. Default FALSE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_leaves.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Adding Leaves to an alignment file w/ accessions — add_leaves","text":"alignment file need two columns: 1. accession + number 2. alignment. protein homolog accession lineage mapping + file alignment file need two columns: 1. accession + number 2. alignment. protein homolog accession lineage mapping + file ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_leaves.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Adding Leaves to an alignment file w/ accessions — add_leaves","text":"Please refer source code alternate + file formats /column names. Please refer source code alternate + file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_leaves.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Adding Leaves to an alignment file w/ accessions — add_leaves","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_leaves.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Adding Leaves to an alignment file w/ accessions — add_leaves","text":"","code":"if (FALSE) { # \\dontrun{ add_leaves(\"pspa_snf7.aln\", \"pspa.txt\") } # } if (FALSE) { # \\dontrun{ add_leaves(\"pspa_snf7.aln\", \"pspa.txt\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_lins.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Lineages — add_lins","title":"Add Lineages — add_lins","text":"Add Lineages add_lins","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_lins.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Lineages — add_lins","text":"","code":"add_lins( df, acc_col = \"AccNum\", assembly_path, lineagelookup_path, ipgout_path = NULL, plan = \"multicore\" ) add_lins( df, acc_col = \"AccNum\", assembly_path, lineagelookup_path, ipgout_path = NULL, plan = \"multicore\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_lins.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Lineages — add_lins","text":"plan","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_lins.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Lineages — add_lins","text":"Describe return, detail","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_lins.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Lineages — add_lins","text":"","code":"if (FALSE) { # \\dontrun{ add_lins() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Name — add_name","title":"Add Name — add_name","text":"function adds new 'Name' column comprised components Kingdom, Phylum, Genus, species, well accession function adds new 'Name' column comprised components Kingdom, Phylum, Genus, species, well accession","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Name — add_name","text":"","code":"add_name( data, accnum_col = \"AccNum\", spec_col = \"Species\", lin_col = \"Lineage\", lin_sep = \">\", out_col = \"Name\" ) add_name( data, accnum_col = \"AccNum\", spec_col = \"Species\", lin_col = \"Lineage\", lin_sep = \">\", out_col = \"Name\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Name — add_name","text":"data Data add name column accnum_col Column containing accession numbers spec_col Column containing species lin_col Column containing lineage lin_sep Character separating lineage levels out_col Column contains new 'Name' derived Species, Lineage, AccNum info","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Name — add_name","text":"Original data 'Name' column Original data 'Name' column","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_name.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Add Name — add_name","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_tax.html","id":null,"dir":"Reference","previous_headings":"","what":"add_tax — add_tax","title":"add_tax — add_tax","text":"add_tax","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_tax.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"add_tax — add_tax","text":"","code":"add_tax(data, acc_col = \"AccNum\", version = T)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/add_tax.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"add_tax — add_tax","text":"version","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/advanced_opts2est_walltime.html","id":null,"dir":"Reference","previous_headings":"","what":"Given MolEvolvR advanced options and number of inputs, calculate the total estimated walltime for the job — advanced_opts2est_walltime","title":"Given MolEvolvR advanced options and number of inputs, calculate the total estimated walltime for the job — advanced_opts2est_walltime","text":"Given MolEvolvR advanced options number inputs, calculate total estimated walltime job","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/advanced_opts2est_walltime.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Given MolEvolvR advanced options and number of inputs, calculate the total estimated walltime for the job — advanced_opts2est_walltime","text":"","code":"advanced_opts2est_walltime( advanced_opts, n_inputs = 1L, n_hits = NULL, verbose = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/advanced_opts2est_walltime.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Given MolEvolvR advanced options and number of inputs, calculate the total estimated walltime for the job — advanced_opts2est_walltime","text":"advanced_opts character vector MolEvolvR advanced options (see make_opts2procs options) n_inputs total number input proteins","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/advanced_opts2est_walltime.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Given MolEvolvR advanced options and number of inputs, calculate the total estimated walltime for the job — advanced_opts2est_walltime","text":"total estimated number seconds job process (walltime) example: advanced_opts2est_walltime(c(\"homology_search\", \"domain_architecture\"), n_inputs = 3, n_hits = 50L)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":null,"dir":"Reference","previous_headings":"","what":"Perform a Multiple Sequence Alignment on a FASTA file. — alignFasta","title":"Perform a Multiple Sequence Alignment on a FASTA file. — alignFasta","text":"Perform Multiple Sequence Alignment FASTA file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Perform a Multiple Sequence Alignment on a FASTA file. — alignFasta","text":"","code":"alignFasta(fasta_file, tool = \"Muscle\", outpath = NULL) alignFasta(fasta_file, tool = \"Muscle\", outpath = NULL)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Perform a Multiple Sequence Alignment on a FASTA file. — alignFasta","text":"fasta_file Path FASTA file aligned tool Type alignment tool use. One three options: \"Muscle\", \"ClustalO\", \"ClustalW\" outpath Path write resulting alignment FASTA file. NULL, file written","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Perform a Multiple Sequence Alignment on a FASTA file. — alignFasta","text":"aligned fasta sequence MsaAAMultipleAlignment object aligned fasta sequence MsaAAMultipleAlignment object","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Perform a Multiple Sequence Alignment on a FASTA file. — alignFasta","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/assert_count_df.html","id":null,"dir":"Reference","previous_headings":"","what":"assert_count_df — assert_count_df","title":"assert_count_df — assert_count_df","text":"assert_count_df","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/assert_count_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"assert_count_df — assert_count_df","text":"","code":"assert_count_df(var)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/assert_count_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"assert_count_df — assert_count_df","text":"var","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/assign_job_queue.html","id":null,"dir":"Reference","previous_headings":"","what":"Decision function to assign job queue — assign_job_queue","title":"Decision function to assign job queue — assign_job_queue","text":"Decision function assign job queue","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/assign_job_queue.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Decision function to assign job queue — assign_job_queue","text":"","code":"assign_job_queue(t_sec_estimate, t_cutoff = 21600)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/assign_job_queue.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Decision function to assign job queue — assign_job_queue","text":"t_sec_estimate estimated number seconds job process (advanced_opts2est_walltime()) t_long threshold value defines lower bound assigning job \"long queue\"","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/assign_job_queue.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Decision function to assign job queue — assign_job_queue","text":"string \"short\" \"long\" example: advanced_opts2est_walltime(c(\"homology_search\", \"domain_architecture\"), 3) |> assign_job_queue()","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/clean_clust_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean Cluster File — clean_clust_file","title":"Clean Cluster File — clean_clust_file","text":"Reads cleans cluster file function reads space-separated cluster file converts cleaned data frame.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/clean_clust_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean Cluster File — clean_clust_file","text":"","code":"clean_clust_file(path, writepath = NULL, query)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/clean_clust_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean Cluster File — clean_clust_file","text":"path character path cluster file cleaned writepath character designating tsv file cleaned cluster file written . value NULL file written. Default NULL query character identifying query file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/clean_clust_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean Cluster File — clean_clust_file","text":"cleaned cluster data frame returned tsv file written \"writepath\" parameter used.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/clean_clust_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Clean Cluster File — clean_clust_file","text":"","code":"if (FALSE) { # \\dontrun{ clean_clust_file(\"data/pspa.op_ins_cls\", writepath = NULL, query = \"pspa\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/clean_string.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean String — clean_string","title":"Clean String — clean_string","text":"Keep alphanumerics, \"\", \"+\", \".\" strings substitute spaces \"\". Used MolEvolvR codebase cleanup domain architecture values","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/clean_string.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean String — clean_string","text":"","code":"clean_string(string)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/clean_string.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean String — clean_string","text":"string","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/clean_string.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean String — clean_string","text":"string string alphanumerics, \"_\", \"+\", \".\"","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/clean_string.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Clean String — clean_string","text":"","code":"if (FALSE) { # \\dontrun{ clean_string() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_GeneDesc.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup GeneDesc — cleanup_GeneDesc","title":"Cleanup GeneDesc — cleanup_GeneDesc","text":"Cleanup GeneDesc","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_GeneDesc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup GeneDesc — cleanup_GeneDesc","text":"","code":"cleanup_GeneDesc(prot, column)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_GeneDesc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup GeneDesc — cleanup_GeneDesc","text":"column","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_GeneDesc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup GeneDesc — cleanup_GeneDesc","text":"Return trailing period occurs GeneDesc column","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_GeneDesc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup GeneDesc — cleanup_GeneDesc","text":"","code":"if (FALSE) { # \\dontrun{ cleanup_GeneDesc() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_clust.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup Clust — cleanup_clust","title":"Cleanup Clust — cleanup_clust","text":"Cleanup cluster file Cleans cluster file removing rows contain query cluster. function removes irrelevant rows contain query protein within ClustName column. return value cleaned data frame.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_clust.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup Clust — cleanup_clust","text":"","code":"cleanup_clust( prot, domains_rename, domains_keep, repeat2s = TRUE, remove_tails = FALSE, remove_empty = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_clust.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup Clust — cleanup_clust","text":"prot data frame must contain columns Query ClustName. domains_rename data frame containing domain names replaced column 'old' corresponding replacement values column 'new'. domains_keep data frame containing domain names retained. repeat2s Boolean. TRUE, repeated domains 'ClustName' condensed. Default TRUE. remove_tails Boolean. TRUE, 'ClustName' filtered based domains keep/remove. Default FALSE. remove_empty Boolean. TRUE, rows empty/unnecessary values 'ClustName' removed. Default FALSE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_clust.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup Clust — cleanup_clust","text":"Cleaned data frame","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_clust.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup Clust — cleanup_clust","text":"","code":"if (FALSE) { # \\dontrun{ cleanup_clust(prot, TRUE, FALSE, domains_keep, domains_rename) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_domarch.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup DomArch — cleanup_domarch","title":"Cleanup DomArch — cleanup_domarch","text":"Cleanup Domain Architectures Cleans DomArch column replacing/removing certain domains function cleans DomArch column one data frame renaming certain domains according second data frame. Certain domains can removed according additional data frame. original data frame returned clean DomArchs column old domains DomArchs.old column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_domarch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup DomArch — cleanup_domarch","text":"","code":"cleanup_domarch( prot, old = \"DomArch.orig\", new = \"DomArch\", domains_keep, domains_rename, repeat2s = TRUE, remove_tails = FALSE, remove_empty = F, domains_ignore = NULL )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_domarch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup DomArch — cleanup_domarch","text":"prot data frame containing 'DomArch' column domains_keep data frame containing domain names retained. domains_rename data frame containing domain names replaced column 'old' corresponding replacement values column 'new'. repeat2s Boolean. TRUE, repeated domains 'DomArch' condensed. Default TRUE. remove_tails Boolean. TRUE, 'ClustName' filtered based domains keep/remove. Default FALSE. remove_empty Boolean. TRUE, rows empty/unnecessary values 'DomArch' removed. Default FALSE. domains_ignore data frame containing domain names removed column called 'domains'","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_domarch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup DomArch — cleanup_domarch","text":"original data frame returned clean DomArchs column old domains DomArchs.old column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_domarch.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup DomArch — cleanup_domarch","text":"","code":"if (FALSE) { # \\dontrun{ cleanup_domarch(prot, TRUE, FALSE, domains_keep, domains_rename, domains_ignore = NULL) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_fasta_header.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup FASTA Header — cleanup_fasta_header","title":"Cleanup FASTA Header — cleanup_fasta_header","text":"Parse accesion numbers fasta add suffix ith occurence handle duplicates","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_fasta_header.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup FASTA Header — cleanup_fasta_header","text":"","code":"cleanup_fasta_header(fasta)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_fasta_header.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup FASTA Header — cleanup_fasta_header","text":"fasta","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_fasta_header.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup FASTA Header — cleanup_fasta_header","text":"XStringSet fasta adjusted names (headers)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_fasta_header.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup FASTA Header — cleanup_fasta_header","text":"","code":"if (FALSE) { # \\dontrun{ AAStringSet(c(\"xxx\" = \"ATCG\", \"xxx\" = \"GGGC\")) |> cleanup_fasta_header() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_gencontext.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup Genomic Contexts — cleanup_gencontext","title":"Cleanup Genomic Contexts — cleanup_gencontext","text":"Cleans GenContext column data frame removing certain characters rows. function removes empty rows based 'GenContext' column. cleaned version data table returned.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_gencontext.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup Genomic Contexts — cleanup_gencontext","text":"","code":"cleanup_gencontext( prot, domains_rename = data.frame(old = character(0), new = character(0), stringsAsFactors = F), repeat2s = TRUE, remove_asterisk = TRUE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_gencontext.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup Genomic Contexts — cleanup_gencontext","text":"prot data frame contains columns 'GenContext.orig' domains_rename data frame containing domain names replaced column 'old' replacement column 'new'. Defaults empty data frame new old column non domains renamed repeat2s Boolean. TRUE, repeated domains 'GenContext' condensed. Default TRUE. remove_asterisk Boolean. TRUE, asterisks 'ClustName' removed. Default TRUE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_gencontext.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup Genomic Contexts — cleanup_gencontext","text":"cleaned version data table returned.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_gencontext.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup Genomic Contexts — cleanup_gencontext","text":"","code":"if (FALSE) { # \\dontrun{ cleanup_gencontext(prot, domains_rename, T, F) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_lineage.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup Lineage — cleanup_lineage","title":"Cleanup Lineage — cleanup_lineage","text":"Cleanup Lineage","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_lineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup Lineage — cleanup_lineage","text":"","code":"cleanup_lineage(prot, lins_rename)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_lineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup Lineage — cleanup_lineage","text":"lins_rename","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_lineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup Lineage — cleanup_lineage","text":"Describe return, detail","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_lineage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup Lineage — cleanup_lineage","text":"","code":"if (FALSE) { # \\dontrun{ cleanup_lineage() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_species.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup Species — cleanup_species","title":"Cleanup Species — cleanup_species","text":"Cleanup Species Cleans species column data frame removing certain characters rows. function removes unneccessary characters 'Species' column. cleaned version data table returned.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_species.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup Species — cleanup_species","text":"","code":"cleanup_species(prot, remove_empty = FALSE)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_species.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup Species — cleanup_species","text":"prot data frame contains columns 'Species'. remove_empty Boolean. TRUE, rows empty/unnecessary values 'Species' removed. Default false.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_species.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup Species — cleanup_species","text":"Describe return, detail","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanup_species.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup Species — cleanup_species","text":"","code":"if (FALSE) { # \\dontrun{ cleanup_species(prot, TRUE) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/combine_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Download the combined assembly summaries of genbank and refseq — combine_files","title":"Download the combined assembly summaries of genbank and refseq — combine_files","text":"Download combined assembly summaries genbank refseq","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combine_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download the combined assembly summaries of genbank and refseq — combine_files","text":"","code":"combine_files( inpath = c(\"../molevol_data/project_data/phage_defense/\"), pattern = \"*full_analysis.tsv\", delim = \"\\t\", skip = 0, col_names = T )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/combine_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download the combined assembly summaries of genbank and refseq — combine_files","text":"inpath String 'master' path files reside (recursive=T) pattern Character vector containing search pattern files col_names Takes logical T/F arguments column names vector; usage similar col_names parameter readr::read_delim","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combine_files.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Download the combined assembly summaries of genbank and refseq — combine_files","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combine_full.html","id":null,"dir":"Reference","previous_headings":"","what":"Combining full_analysis files — combine_full","title":"Combining full_analysis files — combine_full","text":"Combining full_analysis files","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combine_full.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combining full_analysis files — combine_full","text":"","code":"combine_full(inpath, ret = FALSE)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/combine_full.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combining full_analysis files — combine_full","text":"ret","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combine_ipr.html","id":null,"dir":"Reference","previous_headings":"","what":"Combining clean ipr files — combine_ipr","title":"Combining clean ipr files — combine_ipr","text":"Combining clean ipr files","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combine_ipr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combining clean ipr files — combine_ipr","text":"","code":"combine_ipr(inpath, ret = FALSE)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/combine_ipr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combining clean ipr files — combine_ipr","text":"ret","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert_aln2fa.html","id":null,"dir":"Reference","previous_headings":"","what":"Adding Leaves to an alignment file w/ accessions — convert_aln2fa","title":"Adding Leaves to an alignment file w/ accessions — convert_aln2fa","text":"Adding Leaves alignment file w/ accessions Genomic Contexts vs Domain Architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert_aln2fa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adding Leaves to an alignment file w/ accessions — convert_aln2fa","text":"","code":"convert_aln2fa( aln_file = \"\", lin_file = \"data/rawdata_tsv/all_semiclean.txt\", fa_outpath = \"\", reduced = FALSE ) convert_aln2fa( aln_file = \"\", lin_file = \"data/rawdata_tsv/all_semiclean.txt\", fa_outpath = \"\", reduced = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert_aln2fa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Adding Leaves to an alignment file w/ accessions — convert_aln2fa","text":"aln_file Character. Path file. Input tab-delimited file + alignment file accnum & alignment. Default 'pspa_snf7.aln' lin_file Character. Path file. Protein file accession + number lineage mapping. Default 'pspa.txt' fa_outpath Character. Path written fasta file. Default 'NULL' reduced Boolean. TRUE, fasta file contain one sequence per lineage. Default 'FALSE'","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert_aln2fa.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Adding Leaves to an alignment file w/ accessions — convert_aln2fa","text":"alignment file need two columns: 1. accession + number 2. alignment. protein homolog accession lineage mapping + file alignment file need two columns: 1. accession + number 2. alignment. protein homolog accession lineage mapping + file ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert_aln2fa.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Adding Leaves to an alignment file w/ accessions — convert_aln2fa","text":"Please refer source code alternate + file formats /column names. Please refer source code alternate + file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert_aln2fa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Adding Leaves to an alignment file w/ accessions — convert_aln2fa","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert_aln2fa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Adding Leaves to an alignment file w/ accessions — convert_aln2fa","text":"","code":"if (FALSE) { # \\dontrun{ add_leaves(\"pspa_snf7.aln\", \"pspa.txt\") } # } if (FALSE) { # \\dontrun{ add_leaves(\"pspa_snf7.aln\", \"pspa.txt\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert_fa2tre.html","id":null,"dir":"Reference","previous_headings":"","what":"convert_fa2tre — convert_fa2tre","title":"convert_fa2tre — convert_fa2tre","text":"convert_fa2tre","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert_fa2tre.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"convert_fa2tre — convert_fa2tre","text":"","code":"convert_fa2tre( fa_path = here(\"data/alns/pspa_snf7.fa\"), tre_path = here(\"data/alns/pspa_snf7.tre\"), fasttree_path = here(\"src/FastTree\") )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert_fa2tre.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"convert_fa2tre — convert_fa2tre","text":"fasttree_path","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/count_bycol.html","id":null,"dir":"Reference","previous_headings":"","what":"Count Bycol — count_bycol","title":"Count Bycol — count_bycol","text":"Count Bycol","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/count_bycol.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count Bycol — count_bycol","text":"","code":"count_bycol(prot = prot, column = \"DomArch\", min.freq = 1)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/count_bycol.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count Bycol — count_bycol","text":"min.freq","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/count_bycol.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count Bycol — count_bycol","text":"Describe return, detail","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/count_bycol.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count Bycol — count_bycol","text":"","code":"if (FALSE) { # \\dontrun{ count_bycol() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/count_to_sunburst.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an interactive plotly from count data — count_to_sunburst","title":"Create an interactive plotly from count data — count_to_sunburst","text":"functions help quickly create interactive hierarchical plots categorical data. expect summary data created dplyr::count() produce either sunburst plot (count_to_sunburst()) treemap plot (count_to_treemap())","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/count_to_sunburst.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an interactive plotly from count data — count_to_sunburst","text":"","code":"count_to_sunburst( count_data, fill_by_n = FALSE, sort_by_n = FALSE, maxdepth = 2 ) count_to_treemap(count_data, fill_by_n = FALSE, sort_by_n = FALSE)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/count_to_sunburst.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an interactive plotly from count data — count_to_sunburst","text":"count_data fill_by_n TRUE, uses continuous scale fill plot group size sort_by_n","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/count_to_sunburst.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create an interactive plotly from count data — count_to_sunburst","text":"","code":"library(dplyr) #> #> Attaching package: ‘dplyr’ #> The following objects are masked from ‘package:stats’: #> #> filter, lag #> The following objects are masked from ‘package:base’: #> #> intersect, setdiff, setequal, union starwars_count <- count(starwars, species, eye_color, name) # sunburst plot count_to_sunburst(starwars_count) {\"x\":{\"visdat\":{\"40317923875e\":[\"function () \",\"plotlyVisDat\"]},\"cur_data\":\"40317923875e\",\"attrs\":{\"40317923875e\":{\"ids\":[\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",\"NA\",\"Aleena.->.unknown\",\"Besalisk.->.yellow\",\"Cerean.->.yellow\",\"Chagrian.->.blue\",\"Clawdite.->.yellow\",\"Droid.->.black\",\"Droid.->.red\",\"Droid.->.red, blue\",\"Droid.->.yellow\",\"Dug.->.orange\",\"Ewok.->.brown\",\"Geonosian.->.yellow\",\"Gungan.->.orange\",\"Human.->.blue\",\"Human.->.blue-gray\",\"Human.->.brown\",\"Human.->.dark\",\"Human.->.hazel\",\"Human.->.unknown\",\"Human.->.yellow\",\"Hutt.->.orange\",\"Iktotchi.->.orange\",\"Kaleesh.->.green, yellow\",\"Kaminoan.->.black\",\"Kel Dor.->.black\",\"Mirialan.->.blue\",\"Mon Calamari.->.orange\",\"Muun.->.gold\",\"Nautolan.->.black\",\"Neimodian.->.red\",\"Pau'an.->.black\",\"Quermian.->.yellow\",\"Rodian.->.black\",\"Skakoan.->.unknown\",\"Sullustan.->.black\",\"Tholothian.->.blue\",\"Togruta.->.black\",\"Toong.->.orange\",\"Toydarian.->.yellow\",\"Trandoshan.->.red\",\"Twi'lek.->.hazel\",\"Twi'lek.->.pink\",\"Vulptereen.->.yellow\",\"Wookiee.->.blue\",\"Xexto.->.black\",\"Yoda's species.->.brown\",\"Zabrak.->.brown\",\"Zabrak.->.yellow\",\"NA.->.blue\",\"NA.->.brown\",\"NA.->.white\",\"Aleena.->.unknown.->.Ratts Tyerel\",\"Besalisk.->.yellow.->.Dexter Jettster\",\"Cerean.->.yellow.->.Ki-Adi-Mundi\",\"Chagrian.->.blue.->.Mas Amedda\",\"Clawdite.->.yellow.->.Zam Wesell\",\"Droid.->.black.->.BB8\",\"Droid.->.red.->.IG-88\",\"Droid.->.red.->.R2-D2\",\"Droid.->.red.->.R5-D4\",\"Droid.->.red, blue.->.R4-P17\",\"Droid.->.yellow.->.C-3PO\",\"Dug.->.orange.->.Sebulba\",\"Ewok.->.brown.->.Wicket Systri Warrick\",\"Geonosian.->.yellow.->.Poggle the Lesser\",\"Gungan.->.orange.->.Jar Jar Binks\",\"Gungan.->.orange.->.Roos Tarpals\",\"Gungan.->.orange.->.Rugor Nass\",\"Human.->.blue.->.Anakin Skywalker\",\"Human.->.blue.->.Beru Whitesun Lars\",\"Human.->.blue.->.Cliegg Lars\",\"Human.->.blue.->.Finis Valorum\",\"Human.->.blue.->.Jocasta Nu\",\"Human.->.blue.->.Lobot\",\"Human.->.blue.->.Luke Skywalker\",\"Human.->.blue.->.Mon Mothma\",\"Human.->.blue.->.Owen Lars\",\"Human.->.blue.->.Qui-Gon Jinn\",\"Human.->.blue.->.Ric Olié\",\"Human.->.blue.->.Wilhuff Tarkin\",\"Human.->.blue-gray.->.Obi-Wan Kenobi\",\"Human.->.brown.->.Arvel Crynyd\",\"Human.->.brown.->.Bail Prestor Organa\",\"Human.->.brown.->.Biggs Darklighter\",\"Human.->.brown.->.Boba Fett\",\"Human.->.brown.->.Dooku\",\"Human.->.brown.->.Dormé\",\"Human.->.brown.->.Han Solo\",\"Human.->.brown.->.Jango Fett\",\"Human.->.brown.->.Lando Calrissian\",\"Human.->.brown.->.Leia Organa\",\"Human.->.brown.->.Mace Windu\",\"Human.->.brown.->.Padmé Amidala\",\"Human.->.brown.->.Poe Dameron\",\"Human.->.brown.->.Quarsh Panaka\",\"Human.->.brown.->.Raymus Antilles\",\"Human.->.brown.->.Shmi Skywalker\",\"Human.->.dark.->.Finn\",\"Human.->.hazel.->.Rey\",\"Human.->.hazel.->.Wedge Antilles\",\"Human.->.unknown.->.Captain Phasma\",\"Human.->.yellow.->.Darth Vader\",\"Human.->.yellow.->.Palpatine\",\"Hutt.->.orange.->.Jabba Desilijic Tiure\",\"Iktotchi.->.orange.->.Saesee Tiin\",\"Kaleesh.->.green, yellow.->.Grievous\",\"Kaminoan.->.black.->.Lama Su\",\"Kaminoan.->.black.->.Taun We\",\"Kel Dor.->.black.->.Plo Koon\",\"Mirialan.->.blue.->.Barriss Offee\",\"Mirialan.->.blue.->.Luminara Unduli\",\"Mon Calamari.->.orange.->.Ackbar\",\"Muun.->.gold.->.San Hill\",\"Nautolan.->.black.->.Kit Fisto\",\"Neimodian.->.red.->.Nute Gunray\",\"Pau'an.->.black.->.Tion Medon\",\"Quermian.->.yellow.->.Yarael Poof\",\"Rodian.->.black.->.Greedo\",\"Skakoan.->.unknown.->.Wat Tambor\",\"Sullustan.->.black.->.Nien Nunb\",\"Tholothian.->.blue.->.Adi Gallia\",\"Togruta.->.black.->.Shaak Ti\",\"Toong.->.orange.->.Ben Quadinaros\",\"Toydarian.->.yellow.->.Watto\",\"Trandoshan.->.red.->.Bossk\",\"Twi'lek.->.hazel.->.Ayla Secura\",\"Twi'lek.->.pink.->.Bib Fortuna\",\"Vulptereen.->.yellow.->.Dud Bolt\",\"Wookiee.->.blue.->.Chewbacca\",\"Wookiee.->.blue.->.Tarfful\",\"Xexto.->.black.->.Gasgano\",\"Yoda's species.->.brown.->.Yoda\",\"Zabrak.->.brown.->.Eeth Koth\",\"Zabrak.->.yellow.->.Darth Maul\",\"NA.->.blue.->.Jek Tono Porkins\",\"NA.->.brown.->.Cordé\",\"NA.->.brown.->.Gregar Typho\",\"NA.->.white.->.Sly Moore\"],\"parents\":[\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Droid\",\"Droid\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",\"Zabrak\",\"NA\",\"NA\",\"NA\",\"Aleena.->.unknown\",\"Besalisk.->.yellow\",\"Cerean.->.yellow\",\"Chagrian.->.blue\",\"Clawdite.->.yellow\",\"Droid.->.black\",\"Droid.->.red\",\"Droid.->.red\",\"Droid.->.red\",\"Droid.->.red, 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