├── _pkgdown.yml ├── .github ├── .gitignore ├── ISSUE_TEMPLATE.md ├── CONTRIBUTING.md └── workflows │ ├── pkgdown.yaml │ └── R-CMD-check.yaml ├── vignettes ├── .gitignore └── Overview.Rmd ├── .gitignore ├── README_files ├── figure-gfm │ ├── unnamed-chunk-3-1.png │ ├── unnamed-chunk-3-10.png │ ├── unnamed-chunk-3-11.png │ ├── unnamed-chunk-3-12.png │ ├── unnamed-chunk-3-13.png │ ├── unnamed-chunk-3-14.png │ ├── unnamed-chunk-3-15.png │ ├── unnamed-chunk-3-16.png │ ├── unnamed-chunk-3-17.png │ ├── unnamed-chunk-3-18.png │ ├── unnamed-chunk-3-19.png │ ├── unnamed-chunk-3-2.png │ ├── unnamed-chunk-3-20.png │ ├── unnamed-chunk-3-21.png │ ├── unnamed-chunk-3-22.png │ ├── unnamed-chunk-3-23.png │ ├── unnamed-chunk-3-24.png │ ├── unnamed-chunk-3-25.png │ ├── unnamed-chunk-3-26.png │ ├── unnamed-chunk-3-27.png │ ├── unnamed-chunk-3-28.png │ ├── unnamed-chunk-3-29.png │ ├── unnamed-chunk-3-3.png │ ├── unnamed-chunk-3-30.png │ ├── unnamed-chunk-3-31.png │ ├── unnamed-chunk-3-4.png │ ├── unnamed-chunk-3-5.png │ ├── unnamed-chunk-3-6.png │ ├── unnamed-chunk-3-7.png │ ├── unnamed-chunk-3-8.png │ └── unnamed-chunk-3-9.png ├── figure-html │ ├── unnamed-chunk-3-1.png │ ├── unnamed-chunk-3-2.png │ ├── unnamed-chunk-3-3.png │ ├── unnamed-chunk-3-4.png │ ├── unnamed-chunk-3-5.png │ ├── unnamed-chunk-3-6.png │ ├── unnamed-chunk-3-7.png │ ├── unnamed-chunk-3-8.png │ ├── unnamed-chunk-3-9.png │ ├── unnamed-chunk-3-10.png │ ├── unnamed-chunk-3-11.png │ ├── unnamed-chunk-3-12.png │ ├── unnamed-chunk-3-13.png │ ├── unnamed-chunk-3-14.png │ ├── unnamed-chunk-3-15.png │ ├── unnamed-chunk-3-16.png │ ├── unnamed-chunk-3-17.png │ ├── unnamed-chunk-3-18.png │ ├── unnamed-chunk-3-19.png │ ├── unnamed-chunk-3-20.png │ ├── unnamed-chunk-3-21.png │ ├── unnamed-chunk-3-22.png │ ├── unnamed-chunk-3-23.png │ ├── unnamed-chunk-3-24.png │ ├── unnamed-chunk-3-25.png │ ├── unnamed-chunk-3-26.png │ ├── unnamed-chunk-3-27.png │ ├── unnamed-chunk-3-28.png │ ├── unnamed-chunk-3-29.png │ ├── unnamed-chunk-3-30.png │ └── unnamed-chunk-3-31.png ├── bootstrap-3.3.1 │ ├── css │ │ ├── fonts │ │ │ ├── Lato.ttf │ │ │ ├── Ubuntu.ttf │ │ │ ├── LatoBold.ttf │ │ │ ├── OpenSans.ttf │ │ │ ├── Raleway.ttf │ │ │ ├── LatoItalic.ttf │ │ │ ├── NewsCycle.ttf │ │ │ ├── RalewayBold.ttf │ │ │ ├── NewsCycleBold.ttf │ │ │ ├── OpenSansBold.ttf │ │ │ ├── SourceSansPro.ttf │ │ │ ├── OpenSansItalic.ttf │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ ├── SourceSansProBold.ttf │ │ │ └── SourceSansProLight.ttf │ │ ├── bootstrap-theme.min.css │ │ └── bootstrap-theme.css │ ├── fonts │ │ ├── glyphicons-halflings-regular.eot │ │ ├── glyphicons-halflings-regular.ttf │ │ └── glyphicons-halflings-regular.woff │ └── shim │ │ ├── html5shiv.min.js │ │ └── respond.min.js ├── bootstrap-3.3.5 │ ├── css │ │ ├── fonts │ │ │ ├── Lato.ttf │ │ │ ├── Roboto.ttf │ │ │ ├── Ubuntu.ttf │ │ │ ├── LatoBold.ttf │ │ │ ├── OpenSans.ttf │ │ │ ├── Raleway.ttf │ │ │ ├── LatoItalic.ttf │ │ │ ├── NewsCycle.ttf │ │ │ ├── RalewayBold.ttf │ │ │ ├── RobotoBold.ttf │ │ │ ├── RobotoLight.ttf │ │ │ ├── NewsCycleBold.ttf │ │ │ ├── OpenSansBold.ttf │ │ │ ├── OpenSansLight.ttf │ │ │ ├── RobotoMedium.ttf │ │ │ ├── SourceSansPro.ttf │ │ │ ├── OpenSansItalic.ttf │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ ├── SourceSansProBold.ttf │ │ │ ├── SourceSansProLight.ttf │ │ │ ├── OpenSansLightItalic.ttf │ │ │ └── SourceSansProItalic.ttf │ │ ├── bootstrap-theme.min.css │ │ └── bootstrap-theme.css │ ├── fonts │ │ ├── glyphicons-halflings-regular.eot │ │ ├── glyphicons-halflings-regular.ttf │ │ ├── glyphicons-halflings-regular.woff │ │ └── glyphicons-halflings-regular.woff2 │ ├── js │ │ └── npm.js │ └── shim │ │ ├── html5shiv.min.js │ │ └── respond.min.js ├── highlightjs-9.12.0 │ ├── default.css │ └── textmate.css ├── navigation-1.1 │ ├── sourceembed.js │ ├── codefolding.js │ └── tabsets.js ├── highlight │ ├── default.css │ ├── textmate.css │ └── highlight.js ├── highlightjs-1.1 │ ├── default.css │ ├── textmate.css │ └── highlight.js └── navigation-1.0 │ ├── codefolding.js │ └── tabsets.js ├── .Rbuildignore ├── ggord.Rproj ├── NAMESPACE ├── DESCRIPTION ├── README.md └── man └── ggord.Rd /_pkgdown.yml: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.github/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | -------------------------------------------------------------------------------- /vignettes/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | *.R 3 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | inst/doc 5 | -------------------------------------------------------------------------------- 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11 | ^docs$ 12 | ^pkgdown$ 13 | -------------------------------------------------------------------------------- /README_files/highlightjs-9.12.0/default.css: -------------------------------------------------------------------------------- 1 | .hljs-literal { 2 | color: #990073; 3 | } 4 | 5 | .hljs-number { 6 | color: #099; 7 | } 8 | 9 | .hljs-comment { 10 | color: #998; 11 | font-style: italic; 12 | } 13 | 14 | .hljs-keyword { 15 | color: #900; 16 | font-weight: bold; 17 | } 18 | 19 | .hljs-string { 20 | color: #d14; 21 | } 22 | -------------------------------------------------------------------------------- /README_files/highlightjs-9.12.0/textmate.css: -------------------------------------------------------------------------------- 1 | .hljs-literal { 2 | color: rgb(88, 72, 246); 3 | } 4 | 5 | .hljs-number { 6 | color: rgb(0, 0, 205); 7 | } 8 | 9 | .hljs-comment { 10 | color: rgb(76, 136, 107); 11 | } 12 | 13 | .hljs-keyword { 14 | color: rgb(0, 0, 255); 15 | } 16 | 17 | .hljs-string { 18 | color: rgb(3, 106, 7); 19 | } 20 | -------------------------------------------------------------------------------- /README_files/navigation-1.1/sourceembed.js: -------------------------------------------------------------------------------- 1 | 2 | window.initializeSourceEmbed = function(filename) { 3 | $("#rmd-download-source").click(function() { 4 | var src = $("#rmd-source-code").html(); 5 | var a = document.createElement('a'); 6 | a.href = "data:text/x-r-markdown;base64," + src; 7 | a.download = filename; 8 | document.body.appendChild(a); 9 | a.click(); 10 | document.body.removeChild(a); 11 | }); 12 | }; 13 | -------------------------------------------------------------------------------- /ggord.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: knitr 13 | LaTeX: pdfLaTeX 14 | 15 | AutoAppendNewline: Yes 16 | StripTrailingWhitespace: Yes 17 | 18 | BuildType: Package 19 | PackageUseDevtools: Yes 20 | PackageInstallArgs: --no-multiarch --with-keep.source 21 | -------------------------------------------------------------------------------- /README_files/highlight/default.css: -------------------------------------------------------------------------------- 1 | pre .operator, 2 | pre .paren { 3 | color: rgb(104, 118, 135) 4 | } 5 | 6 | pre .literal { 7 | color: #990073 8 | } 9 | 10 | pre .number { 11 | color: #099; 12 | } 13 | 14 | pre .comment { 15 | color: #998; 16 | font-style: italic 17 | } 18 | 19 | pre .keyword { 20 | color: #900; 21 | font-weight: bold 22 | } 23 | 24 | pre .identifier { 25 | color: rgb(0, 0, 0); 26 | } 27 | 28 | pre .string { 29 | color: #d14; 30 | } 31 | -------------------------------------------------------------------------------- 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| } 17 | 18 | pre .keyword { 19 | color: rgb(0, 0, 255); 20 | } 21 | 22 | pre .identifier { 23 | color: rgb(0, 0, 0); 24 | } 25 | 26 | pre .string { 27 | color: rgb(3, 106, 7); 28 | } 29 | 30 | -------------------------------------------------------------------------------- /README_files/highlightjs-1.1/textmate.css: -------------------------------------------------------------------------------- 1 | pre .operator, 2 | pre .paren { 3 | color: rgb(104, 118, 135) 4 | } 5 | 6 | pre .literal { 7 | color: rgb(88, 72, 246) 8 | } 9 | 10 | pre .number { 11 | color: rgb(0, 0, 205); 12 | } 13 | 14 | pre .comment { 15 | color: rgb(76, 136, 107); 16 | } 17 | 18 | pre .keyword { 19 | color: rgb(0, 0, 255); 20 | } 21 | 22 | pre .identifier { 23 | color: rgb(0, 0, 0); 24 | } 25 | 26 | pre .string { 27 | color: rgb(3, 106, 7); 28 | } 29 | 30 | -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- 1 | # Generated by roxygen2: do not edit by hand 2 | 3 | S3method(ggord,MCA) 4 | S3method(ggord,PCA) 5 | S3method(ggord,acm) 6 | S3method(ggord,ca) 7 | S3method(ggord,capscale) 8 | S3method(ggord,cca) 9 | S3method(ggord,coa) 10 | S3method(ggord,dbrda) 11 | S3method(ggord,default) 12 | S3method(ggord,dpcoa) 13 | S3method(ggord,lda) 14 | S3method(ggord,mca) 15 | S3method(ggord,metaMDS) 16 | S3method(ggord,pca) 17 | S3method(ggord,ppca) 18 | S3method(ggord,prcomp) 19 | S3method(ggord,princomp) 20 | S3method(ggord,rda) 21 | export(ggord) 22 | import(ggplot2) 23 | -------------------------------------------------------------------------------- /README_files/bootstrap-3.3.5/js/npm.js: -------------------------------------------------------------------------------- 1 | // This file is autogenerated via the `commonjs` Grunt task. You can require() this file in a CommonJS environment. 2 | require('../../js/transition.js') 3 | require('../../js/alert.js') 4 | require('../../js/button.js') 5 | require('../../js/carousel.js') 6 | require('../../js/collapse.js') 7 | require('../../js/dropdown.js') 8 | require('../../js/modal.js') 9 | require('../../js/tooltip.js') 10 | require('../../js/popover.js') 11 | require('../../js/scrollspy.js') 12 | require('../../js/tab.js') 13 | require('../../js/affix.js') -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE.md: -------------------------------------------------------------------------------- 1 | # Issues 2 | 3 | Any issues or feature requests can be posted on the [issues](https://github.com/fawda123/ggord/issues) page. Please briefly describe your problem and what output you expect. If you have a question, please don't use this form. Instead, ask on or send me a direct message. 4 | 5 | Please include a minimal reproducible example (AKA a reprex). If you've never heard of a [reprex](https://reprex.tidyverse.org/) before, start by reading . 6 | 7 | --- 8 | 9 | Brief description of the problem 10 | 11 | ```r 12 | # insert reprex here 13 | ``` 14 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: ggord 2 | Type: Package 3 | Title: Ordination Plots with ggplot2 4 | Version: 1.1.8 5 | Date: 2024-07-16 6 | Author: Marcus W. Beck [aut, cre] 7 | Maintainer: Marcus W. Beck 8 | Description: Create ordination biplots with ggplot2. Multiple methods are 9 | available including principal components analysis, correspondence analysis, 10 | nonmetric multidimensional scaling, multiple correspondence analysis, and linear 11 | discriminant analysis. Limited triplot methods are also available. 12 | BugReports: https://github.com/fawda123/ggord/issues 13 | License: CC0 14 | LazyData: true 15 | Imports: 16 | ggplot2, 17 | ggrepel, 18 | grid, 19 | plyr 20 | Depends: 21 | R (>= 3.1.1) 22 | Suggests: 23 | knitr, 24 | ade4, 25 | adephylo, 26 | ape, 27 | ca, 28 | FactoMineR, 29 | MASS, 30 | phylobase, 31 | vegan, 32 | rmarkdown 33 | Authors@R: person(given = "Marcus W.", family = "Beck", 34 | role = c("aut","cre"), 35 | email = "mbafs2012@gmail.com") 36 | RoxygenNote: 7.2.3 37 | VignetteBuilder: knitr 38 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | ## ggord 3 | 4 | #### *Marcus W. Beck, * 5 | 6 | [![R-CMD-check](https://github.com/fawda123/ggord/workflows/R-CMD-check/badge.svg)](https://github.com/fawda123/ggord/actions) 7 | [![DOI](https://zenodo.org/badge/35334615.svg)](https://zenodo.org/badge/latestdoi/35334615) 8 | 9 | A simple package for creating ordination plots with ggplot2. View the website for an overview: 10 | 11 | ### Installation 12 | 13 | Install the package as follows: 14 | 15 | ``` r 16 | # Enable the r-universe repo 17 | options(repos = c( 18 | fawda123 = 'https://fawda123.r-universe.dev', 19 | CRAN = 'https://cloud.r-project.org')) 20 | 21 | # Install ggord 22 | install.packages('ggord') 23 | ``` 24 | 25 | ### Citation 26 | 27 | Please cite the current release as follows: 28 | 29 | Marcus W. Beck (2024). ggord: Ordination Plots with ggplot2. R package 30 | version 1.1.8. 31 | 32 | ### Contribution and issues 33 | 34 | For making contributions to this package, please see the instructions on 35 | the [contributing](.github/CONTRIBUTING.md) page. 36 | 37 | For bugs or feature requests, please follow the instructions 38 | [here](.github/ISSUE_TEMPLATE.md). 39 | -------------------------------------------------------------------------------- /.github/CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | # Contributing to ggord 2 | 3 | This outlines how to propose a change to ggord. 4 | 5 | ### Fixing typos 6 | 7 | Small typos or grammatical errors in documentation may be edited directly using 8 | the GitHub web interface, so long as the changes are made in the _source_ file. 9 | 10 | * YES: you edit a roxygen comment in a `.R` file below `R/`. 11 | * NO: you edit an `.Rd` file below `man/`. 12 | 13 | ### Prerequisites 14 | 15 | Before you make a substantial pull request, you should always file an issue and 16 | make sure someone from the team agrees that it’s a problem. If you’ve found a 17 | bug, create an associated issue and illustrate the bug with a minimal 18 | [reprex](https://www.tidyverse.org/help/#reprex). 19 | 20 | ### Pull request process 21 | 22 | * We recommend that you create a Git branch for each pull request (PR). 23 | * Look at the Travis and AppVeyor build status before and after making changes. 24 | The `README` should contain badges for any continuous integration services used 25 | by the package. 26 | * New code should follow the tidyverse [style guide](http://style.tidyverse.org). 27 | You can use the [styler](https://CRAN.R-project.org/package=styler) package to 28 | apply these styles, but please don't restyle code that has nothing to do with 29 | your PR. 30 | * We use [roxygen2](https://cran.r-project.org/package=roxygen2), with 31 | [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/markdown.html), 32 | for documentation. 33 | -------------------------------------------------------------------------------- /.github/workflows/pkgdown.yaml: -------------------------------------------------------------------------------- 1 | # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples 2 | # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help 3 | on: 4 | push: 5 | branches: [main, master] 6 | pull_request: 7 | branches: [main, master] 8 | release: 9 | types: [published] 10 | workflow_dispatch: 11 | 12 | name: pkgdown 13 | 14 | permissions: read-all 15 | 16 | jobs: 17 | pkgdown: 18 | runs-on: ubuntu-latest 19 | # Only restrict concurrency for non-PR jobs 20 | concurrency: 21 | group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} 22 | env: 23 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} 24 | permissions: 25 | contents: write 26 | steps: 27 | - uses: actions/checkout@v4 28 | 29 | - uses: r-lib/actions/setup-pandoc@v2 30 | 31 | - uses: r-lib/actions/setup-r@v2 32 | with: 33 | use-public-rspm: true 34 | 35 | - uses: r-lib/actions/setup-r-dependencies@v2 36 | with: 37 | extra-packages: any::pkgdown, local::. 38 | needs: website 39 | 40 | - name: Build site 41 | run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) 42 | shell: Rscript {0} 43 | 44 | - name: Deploy to GitHub pages 🚀 45 | if: github.event_name != 'pull_request' 46 | uses: JamesIves/github-pages-deploy-action@v4.5.0 47 | with: 48 | clean: false 49 | branch: gh-pages 50 | folder: docs 51 | -------------------------------------------------------------------------------- /.github/workflows/R-CMD-check.yaml: -------------------------------------------------------------------------------- 1 | # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples 2 | # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help 3 | on: 4 | push: 5 | branches: [main, master] 6 | pull_request: 7 | branches: [main, master] 8 | 9 | name: R-CMD-check 10 | 11 | permissions: read-all 12 | 13 | jobs: 14 | R-CMD-check: 15 | runs-on: ${{ matrix.config.os }} 16 | 17 | name: ${{ matrix.config.os }} (${{ matrix.config.r }}) 18 | 19 | strategy: 20 | fail-fast: false 21 | matrix: 22 | config: 23 | - {os: macos-latest, r: 'release'} 24 | - {os: windows-latest, r: 'release'} 25 | - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} 26 | - {os: ubuntu-latest, r: 'release'} 27 | - {os: ubuntu-latest, r: 'oldrel-1'} 28 | 29 | env: 30 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} 31 | R_KEEP_PKG_SOURCE: yes 32 | 33 | steps: 34 | - uses: actions/checkout@v4 35 | 36 | - uses: r-lib/actions/setup-pandoc@v2 37 | 38 | - uses: r-lib/actions/setup-r@v2 39 | with: 40 | r-version: ${{ matrix.config.r }} 41 | http-user-agent: ${{ matrix.config.http-user-agent }} 42 | use-public-rspm: true 43 | 44 | - uses: r-lib/actions/setup-r-dependencies@v2 45 | with: 46 | extra-packages: any::rcmdcheck 47 | needs: check 48 | 49 | - uses: r-lib/actions/check-r-package@v2 50 | with: 51 | upload-snapshots: true 52 | build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' 53 | -------------------------------------------------------------------------------- /README_files/navigation-1.0/codefolding.js: -------------------------------------------------------------------------------- 1 | 2 | 3 | window.initializeCodeFolding = function(show) { 4 | 5 | // handlers for show-all and hide all 6 | $("#rmd-show-all-code").click(function() { 7 | $('div.r-code-collapse').each(function() { 8 | $(this).collapse('show'); 9 | }); 10 | }); 11 | $("#rmd-hide-all-code").click(function() { 12 | $('div.r-code-collapse').each(function() { 13 | $(this).collapse('hide'); 14 | }); 15 | }); 16 | 17 | // index for unique code element ids 18 | var currentIndex = 1; 19 | 20 | // select all R code blocks 21 | var rCodeBlocks = $('pre.r'); 22 | rCodeBlocks.each(function() { 23 | 24 | // create a collapsable div to wrap the code in 25 | var div = $('
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7 | }; 8 | -------------------------------------------------------------------------------- /README_files/navigation-1.0/tabsets.js: -------------------------------------------------------------------------------- 1 | 2 | 3 | window.buildTabsets = function(tocID) { 4 | 5 | // build a tabset from a section div with the .tabset class 6 | function buildTabset(tabset) { 7 | 8 | // check for fade and pills options 9 | var fade = tabset.hasClass("tabset-fade"); 10 | var pills = tabset.hasClass("tabset-pills"); 11 | var navClass = pills ? "nav-pills" : "nav-tabs"; 12 | 13 | // determine the heading level of the tabset and tabs 14 | var match = tabset.attr('class').match(/level(\d) /); 15 | if (match === null) 16 | return; 17 | var tabsetLevel = Number(match[1]); 18 | var tabLevel = tabsetLevel + 1; 19 | 20 | // find all subheadings immediately below 21 | var tabs = tabset.find("div.section.level" + tabLevel); 22 | if (!tabs.length) 23 | return; 24 | 25 | // create tablist and tab-content elements 26 | var tabList = $('
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12 | $.fn.rmarkdownStickyTabs = function() { 13 | var context = this; 14 | // Show the tab corresponding with the hash in the URL, or the first tab 15 | var showStuffFromHash = function() { 16 | var hash = window.location.hash; 17 | var selector = hash ? 'a[href="' + hash + '"]' : 'li.active > a'; 18 | var $selector = $(selector, context); 19 | if($selector.data('toggle') === "tab") { 20 | $selector.tab('show'); 21 | // walk up the ancestors of this element, show any hidden tabs 22 | $selector.parents('.section.tabset').each(function(i, elm) { 23 | var link = $('a[href="#' + $(elm).attr('id') + '"]'); 24 | if(link.data('toggle') === "tab") { 25 | link.tab("show"); 26 | } 27 | }); 28 | } 29 | }; 30 | 31 | 32 | // Set the correct tab when the page loads 33 | showStuffFromHash(context); 34 | 35 | // Set the correct tab when a user uses their back/forward button 36 | $(window).on('hashchange', function() { 37 | showStuffFromHash(context); 38 | }); 39 | 40 | // Change the URL when tabs are clicked 41 | $('a', context).on('click', function(e) { 42 | history.pushState(null, null, this.href); 43 | showStuffFromHash(context); 44 | }); 45 | 46 | return this; 47 | }; 48 | }(jQuery)); 49 | 50 | window.buildTabsets = function(tocID) { 51 | 52 | // build a tabset from a section div with the .tabset class 53 | function buildTabset(tabset) { 54 | 55 | // check for fade and pills options 56 | var fade = tabset.hasClass("tabset-fade"); 57 | var pills = tabset.hasClass("tabset-pills"); 58 | var navClass = pills ? "nav-pills" : "nav-tabs"; 59 | 60 | // determine the heading level of the tabset and tabs 61 | var match = tabset.attr('class').match(/level(\d) /); 62 | if (match === null) 63 | return; 64 | var tabsetLevel = Number(match[1]); 65 | var tabLevel = tabsetLevel + 1; 66 | 67 | // find all subheadings immediately below 68 | var tabs = tabset.find("div.section.level" + tabLevel); 69 | if (!tabs.length) 70 | return; 71 | 72 | // create tablist and tab-content elements 73 | var tabList = $('
      '); 74 | $(tabs[0]).before(tabList); 75 | var tabContent = $('
      '); 76 | $(tabs[0]).before(tabContent); 77 | 78 | // build the tabset 79 | var activeTab = 0; 80 | tabs.each(function(i) { 81 | 82 | // get the tab div 83 | var tab = $(tabs[i]); 84 | 85 | // get the id then sanitize it for use with bootstrap tabs 86 | var id = tab.attr('id'); 87 | 88 | // see if this is marked as the active tab 89 | if (tab.hasClass('active')) 90 | activeTab = i; 91 | 92 | // remove any table of contents entries associated with 93 | // this ID (since we'll be removing the heading element) 94 | $("div#" + tocID + " li a[href='#" + id + "']").parent().remove(); 95 | 96 | // sanitize the id for use with bootstrap tabs 97 | id = id.replace(/[.\/?&!#<>]/g, '').replace(/\s/g, '_'); 98 | tab.attr('id', id); 99 | 100 | // get the heading element within it, grab it's text, then remove it 101 | var heading = tab.find('h' + tabLevel + ':first'); 102 | var headingText = heading.html(); 103 | heading.remove(); 104 | 105 | // build and append the tab list item 106 | var a = $('' + headingText + ''); 107 | a.attr('href', '#' + id); 108 | a.attr('aria-controls', id); 109 | var li = $('
    • '); 110 | li.append(a); 111 | tabList.append(li); 112 | 113 | // set it's attributes 114 | tab.attr('role', 'tabpanel'); 115 | tab.addClass('tab-pane'); 116 | tab.addClass('tabbed-pane'); 117 | if (fade) 118 | tab.addClass('fade'); 119 | 120 | // move it into the tab content div 121 | tab.detach().appendTo(tabContent); 122 | }); 123 | 124 | // set active tab 125 | $(tabList.children('li')[activeTab]).addClass('active'); 126 | var active = $(tabContent.children('div.section')[activeTab]); 127 | active.addClass('active'); 128 | if (fade) 129 | active.addClass('in'); 130 | 131 | if (tabset.hasClass("tabset-sticky")) 132 | tabset.rmarkdownStickyTabs(); 133 | } 134 | 135 | // convert section divs with the .tabset class to tabsets 136 | var tabsets = $("div.section.tabset"); 137 | tabsets.each(function(i) { 138 | buildTabset($(tabsets[i])); 139 | }); 140 | }; 141 | 142 | -------------------------------------------------------------------------------- /vignettes/Overview.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Overview" 3 | output: rmarkdown::html_vignette 4 | vignette: > 5 | %\VignetteIndexEntry{Overview} 6 | %\VignetteEngine{knitr::rmarkdown} 7 | %\VignetteEncoding{UTF-8} 8 | --- 9 | 10 | ```{r, include = FALSE} 11 | knitr::opts_chunk$set( 12 | collapse = TRUE, 13 | message = FALSE, 14 | warning = FALSE, 15 | comment = "#>" 16 | ) 17 | ``` 18 | 19 | ### Usage 20 | 21 | The following shows some examples of creating biplots using the methods available with ggord. These methods were developed independently from the [ggbiplot](https://github.com/vqv/ggbiplot) and [factoextra](https://github.com/kassambara/factoextra) packages, though the biplots are practically identical. Most methods are for results from principal components analysis, although methods are available for nonmetric multidimensional scaling, multiple correspondence analysis, correspondence analysis, and linear discriminant analysis. Available methods are as follows: 22 | ```{r, echo = FALSE, message = F, warning = F} 23 | library(ggord) 24 | methods('ggord') 25 | ``` 26 | ```{r fig.height = 7, fig.width = 7, message = FALSE, warning = F, results = 'hide'} 27 | # principal components analysis with the iris data set 28 | # prcomp 29 | ord <- prcomp(iris[, 1:4]) 30 | 31 | p <- ggord(ord, iris$Species) 32 | p 33 | 34 | p <- ggord(ord, iris$Species, cols = c('purple', 'orange', 'blue')) 35 | p 36 | 37 | library(ggplot2) 38 | p + scale_shape_manual('Groups', values = c(1, 2, 3)) 39 | p + theme_classic() 40 | p + theme(legend.position = 'top') 41 | 42 | # transparent ellipses 43 | p <- ggord(ord, iris$Species, poly = FALSE) 44 | p 45 | 46 | # change linetype for transparent ellipses 47 | p <- ggord(ord, iris$Species, poly = FALSE, polylntyp = iris$Species) 48 | p 49 | 50 | # convex hulls 51 | p <- ggord(ord, iris$Species, ellipse = FALSE, hull = TRUE) 52 | p 53 | 54 | # change the vector labels with vec_lab 55 | new_lab <- list(Sepal.Length = 'SL', Sepal.Width = 'SW', Petal.Width = 'PW', 56 | Petal.Length = 'PL') 57 | p <- ggord(ord, iris$Species, vec_lab = new_lab) 58 | p 59 | 60 | # observations as labels from row names 61 | p <- ggord(ord, iris$Species, obslab = TRUE) 62 | p 63 | 64 | # map a variable to point sizes 65 | p <- ggord(ord, grp_in = iris$Species, size = iris$Sepal.Length, sizelab = 'Sepal\nlength') 66 | p 67 | 68 | # change vector scaling, arrow length, line color, size, and type 69 | p <- ggord(ord, grp_in = iris$Species, arrow = 1, vec_ext = 3, veccol = 'red', veclsz = 1, vectyp = 'dotted') 70 | p 71 | 72 | # change color of text labels on vectors, use ggrepel to prevent text overlap 73 | p <- ggord(ord, grp_in = iris$Species, labcol = 'purple', repel = TRUE) 74 | p 75 | 76 | # faceted by group 77 | p <- ggord(ord, iris$Species, facet = TRUE, nfac = 1) 78 | p 79 | 80 | # principal components analysis with the iris dataset 81 | # princomp 82 | ord <- princomp(iris[, 1:4]) 83 | 84 | ggord(ord, iris$Species) 85 | 86 | # principal components analysis with the iris dataset 87 | # PCA 88 | library(FactoMineR) 89 | 90 | ord <- PCA(iris[, 1:4], graph = FALSE) 91 | 92 | ggord(ord, iris$Species) 93 | 94 | # principal components analysis with the iris dataset 95 | # dudi.pca 96 | library(ade4) 97 | 98 | ord <- dudi.pca(iris[, 1:4], scannf = FALSE, nf = 4) 99 | 100 | ggord(ord, iris$Species) 101 | 102 | # multiple correspondence analysis with the tea dataset 103 | # MCA 104 | data(tea, package = 'FactoMineR') 105 | tea <- tea[, c('Tea', 'sugar', 'price', 'age_Q', 'sex')] 106 | 107 | ord <- MCA(tea[, -1], graph = FALSE) 108 | 109 | ggord(ord, tea$Tea, parse = FALSE) # use parse = FALSE for labels with non alphanumeric characters 110 | 111 | # multiple correspondence analysis with the tea dataset 112 | # mca 113 | library(MASS) 114 | 115 | ord <- mca(tea[, -1]) 116 | 117 | ggord(ord, tea$Tea, parse = FALSE) # use parse = FALSE for labels with non alphanumeric characters 118 | 119 | # multiple correspondence analysis with the tea dataset 120 | # acm 121 | ord <- dudi.acm(tea[, -1], scannf = FALSE) 122 | 123 | ggord(ord, tea$Tea, parse = FALSE) # use parse = FALSE for labels with non alphanumeric characters 124 | 125 | # nonmetric multidimensional scaling with the iris dataset 126 | # metaMDS 127 | library(vegan) 128 | ord <- metaMDS(iris[, 1:4]) 129 | 130 | ggord(ord, iris$Species) 131 | 132 | # linear discriminant analysis 133 | # example from lda in MASS package 134 | ord <- lda(Species ~ ., iris, prior = rep(1, 3)/3) 135 | 136 | ggord(ord, iris$Species) 137 | 138 | # correspondence analysis 139 | # dudi.coa 140 | ord <- dudi.coa(iris[, 1:4], scannf = FALSE, nf = 4) 141 | 142 | ggord(ord, iris$Species) 143 | 144 | # correspondence analysis 145 | # ca 146 | library(ca) 147 | ord <- ca(iris[, 1:4]) 148 | 149 | ggord(ord, iris$Species) 150 | 151 | # double principle coordinate analysis (DPCoA) 152 | # dpcoa 153 | library(ade4) 154 | data(ecomor) 155 | grp <- rep(c("Bu", "Ca", "Ch", "Pr"), each = 4) # sample groups 156 | dtaxo <- dist.taxo(ecomor$taxo) # taxonomic distance between species 157 | ord <- dpcoa(data.frame(t(ecomor$habitat)), dtaxo, scan = FALSE, nf = 2) 158 | 159 | ggord(ord, grp_in = grp, ellipse = FALSE, arrow = 0.2, txt = 3) 160 | 161 | # phylogenetic PCA 162 | # ppca 163 | library(adephylo) 164 | library(phylobase) 165 | library(ape) 166 | 167 | data(lizards) 168 | 169 | # example from help file, adephylo::ppca 170 | # original example from JOMBART ET AL 2010 171 | 172 | # build a tree and phylo4d object 173 | liz.tre <- read.tree(tex=lizards$hprA) 174 | liz.4d <- phylobase::phylo4d(liz.tre, lizards$traits) 175 | 176 | # remove duplicated populations 177 | liz.4d <- phylobase::prune(liz.4d, c(7,14)) 178 | 179 | 180 | # correct labels 181 | lab <- c("Pa", "Ph", "Ll", "Lmca", "Lmcy", "Phha", "Pha", 182 | "Pb", "Pm", "Ae", "Tt", "Ts", "Lviv", "La", "Ls", "Lvir") 183 | tipLabels(liz.4d) <- lab 184 | 185 | # remove size effect 186 | dat <- tdata(liz.4d, type="tip") 187 | dat <- log(dat) 188 | newdat <- data.frame(lapply(dat, function(v) residuals(lm(v~dat$mean.L)))) 189 | rownames(newdat) <- rownames(dat) 190 | tdata(liz.4d, type="tip") <- newdat[,-1] # replace data in the phylo4d object 191 | 192 | # create ppca 193 | liz.ppca <- ppca(liz.4d,scale=FALSE,scannf=FALSE,nfposi=1,nfnega=1, method="Abouheif") 194 | 195 | # plot 196 | ggord(liz.ppca) 197 | 198 | # distance-based redundancy analysis 199 | # dbrda from vegan 200 | data(varespec) 201 | data(varechem) 202 | 203 | ord <- dbrda(varespec ~ N + P + K + Condition(Al), varechem, dist = "bray") 204 | 205 | ggord(ord) 206 | 207 | ###### 208 | # triplots 209 | 210 | # redundancy analysis 211 | # rda from vegan 212 | ord <- rda(varespec, varechem) 213 | 214 | ggord(ord) 215 | 216 | # distance-based redundancy analysis 217 | # capscale from vegan 218 | ord <- capscale(varespec ~ N + P + K + Condition(Al), varechem, dist = "bray") 219 | 220 | ggord(ord) 221 | 222 | # canonical correspondence analysis 223 | # cca from vegan 224 | ord <- cca(varespec, varechem) 225 | 226 | ggord(ord) 227 | 228 | # species points as text 229 | # suppress site points 230 | ggord(ord, ptslab = TRUE, size = NA, addsize = 5, parse = TRUE) 231 | ``` 232 | -------------------------------------------------------------------------------- /README_files/highlight/highlight.js: -------------------------------------------------------------------------------- 1 | 2 | var hljs=new function(){function m(p){return p.replace(/&/gm,"&").replace(/"}while(y.length||w.length){var v=u().splice(0,1)[0];z+=m(x.substr(q,v.offset-q));q=v.offset;if(v.event=="start"){z+=t(v.node);s.push(v.node)}else{if(v.event=="stop"){var p,r=s.length;do{r--;p=s[r];z+=("")}while(p!=v.node);s.splice(r,1);while(r'+M[0]+""}else{r+=M[0]}O=P.lR.lastIndex;M=P.lR.exec(L)}return r+L.substr(O,L.length-O)}function J(L,M){if(M.sL&&e[M.sL]){var r=d(M.sL,L);x+=r.keyword_count;return r.value}else{return F(L,M)}}function I(M,r){var L=M.cN?'':"";if(M.rB){y+=L;M.buffer=""}else{if(M.eB){y+=m(r)+L;M.buffer=""}else{y+=L;M.buffer=r}}D.push(M);A+=M.r}function G(N,M,Q){var R=D[D.length-1];if(Q){y+=J(R.buffer+N,R);return false}var P=q(M,R);if(P){y+=J(R.buffer+N,R);I(P,M);return P.rB}var L=v(D.length-1,M);if(L){var O=R.cN?"":"";if(R.rE){y+=J(R.buffer+N,R)+O}else{if(R.eE){y+=J(R.buffer+N,R)+O+m(M)}else{y+=J(R.buffer+N+M,R)+O}}while(L>1){O=D[D.length-2].cN?"":"";y+=O;L--;D.length--}var r=D[D.length-1];D.length--;D[D.length-1].buffer="";if(r.starts){I(r.starts,"")}return R.rE}if(w(M,R)){throw"Illegal"}}var E=e[B];var D=[E.dM];var A=0;var x=0;var y="";try{var s,u=0;E.dM.buffer="";do{s=p(C,u);var t=G(s[0],s[1],s[2]);u+=s[0].length;if(!t){u+=s[1].length}}while(!s[2]);if(D.length>1){throw"Illegal"}return{r:A,keyword_count:x,value:y}}catch(H){if(H=="Illegal"){return{r:0,keyword_count:0,value:m(C)}}else{throw H}}}function g(t){var p={keyword_count:0,r:0,value:m(t)};var r=p;for(var q in e){if(!e.hasOwnProperty(q)){continue}var s=d(q,t);s.language=q;if(s.keyword_count+s.r>r.keyword_count+r.r){r=s}if(s.keyword_count+s.r>p.keyword_count+p.r){r=p;p=s}}if(r.language){p.second_best=r}return p}function i(r,q,p){if(q){r=r.replace(/^((<[^>]+>|\t)+)/gm,function(t,w,v,u){return w.replace(/\t/g,q)})}if(p){r=r.replace(/\n/g,"
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3 | hljs.initHighlightingOnLoad(); 4 | 5 | -------------------------------------------------------------------------------- /man/ggord.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/ggord.R 3 | \name{ggord} 4 | \alias{ggord} 5 | \alias{ggord.default} 6 | \alias{ggord.PCA} 7 | \alias{ggord.MCA} 8 | \alias{ggord.mca} 9 | \alias{ggord.acm} 10 | \alias{ggord.prcomp} 11 | \alias{ggord.princomp} 12 | \alias{ggord.metaMDS} 13 | \alias{ggord.lda} 14 | \alias{ggord.pca} 15 | \alias{ggord.coa} 16 | \alias{ggord.ca} 17 | \alias{ggord.ppca} 18 | \alias{ggord.rda} 19 | \alias{ggord.capscale} 20 | \alias{ggord.dbrda} 21 | \alias{ggord.cca} 22 | \alias{ggord.dpcoa} 23 | \title{Ordination plots with ggplot2} 24 | \usage{ 25 | ggord(...) 26 | 27 | \method{ggord}{default}( 28 | obs, 29 | vecs, 30 | axes = c("1", "2"), 31 | grp_in = NULL, 32 | cols = NULL, 33 | facet = FALSE, 34 | nfac = NULL, 35 | addpts = NULL, 36 | obslab = FALSE, 37 | ptslab = FALSE, 38 | ellipse = TRUE, 39 | ellipse_pro = 0.95, 40 | poly = TRUE, 41 | polylntyp = "solid", 42 | hull = FALSE, 43 | arrow = 0.4, 44 | labcol = "black", 45 | veccol = "black", 46 | vectyp = "solid", 47 | veclsz = 0.5, 48 | ext = 1.2, 49 | repel = FALSE, 50 | vec_ext = 1, 51 | vec_lab = NULL, 52 | size = 4, 53 | sizelab = NULL, 54 | addsize = size/2, 55 | addcol = "blue", 56 | addpch = 19, 57 | txt = 4, 58 | alpha = 1, 59 | alpha_el = 0.4, 60 | xlims = NULL, 61 | ylims = NULL, 62 | var_sub = NULL, 63 | coord_fix = TRUE, 64 | parse = TRUE, 65 | grp_title = "Groups", 66 | force = 1, 67 | max.overlaps = 10, 68 | exp = c(0, 0), 69 | ... 70 | ) 71 | 72 | \method{ggord}{PCA}(ord_in, grp_in = NULL, axes = c("1", "2"), ...) 73 | 74 | \method{ggord}{MCA}(ord_in, grp_in = NULL, axes = c("1", "2"), ...) 75 | 76 | \method{ggord}{mca}(ord_in, grp_in = NULL, axes = c("1", "2"), ...) 77 | 78 | \method{ggord}{acm}(ord_in, grp_in = NULL, axes = c("1", "2"), ...) 79 | 80 | \method{ggord}{prcomp}(ord_in, grp_in = NULL, axes = c("1", "2"), ...) 81 | 82 | \method{ggord}{princomp}(ord_in, grp_in = NULL, axes = c("1", "2"), ...) 83 | 84 | \method{ggord}{metaMDS}(ord_in, grp_in = NULL, axes = c("1", "2"), ...) 85 | 86 | \method{ggord}{lda}(ord_in, grp_in = NULL, axes = c("1", "2"), ...) 87 | 88 | \method{ggord}{pca}(ord_in, grp_in = NULL, axes = c("1", "2"), ...) 89 | 90 | \method{ggord}{coa}(ord_in, grp_in = NULL, axes = c("1", "2"), ...) 91 | 92 | \method{ggord}{ca}(ord_in, grp_in = NULL, axes = c("1", "2"), ...) 93 | 94 | \method{ggord}{ppca}(ord_in, grp_in = NULL, axes = NULL, ...) 95 | 96 | \method{ggord}{rda}(ord_in, grp_in = NULL, axes = c("1", "2"), ...) 97 | 98 | \method{ggord}{capscale}(ord_in, grp_in = NULL, axes = c("1", "2"), ...) 99 | 100 | \method{ggord}{dbrda}(ord_in, grp_in = NULL, axes = c("1", "2"), ...) 101 | 102 | \method{ggord}{cca}(ord_in, grp_in = NULL, axes = c("1", "2"), ...) 103 | 104 | \method{ggord}{dpcoa}(ord_in, grp_in = NULL, axes = c("1", "2"), ...) 105 | } 106 | \arguments{ 107 | \item{...}{arguments passed to or from other methods} 108 | 109 | \item{obs}{matrix or data frame of axis scores for each observation} 110 | 111 | \item{vecs}{matrix or data frame of axis scores for each variable} 112 | 113 | \item{axes}{chr string indicating which axes to plot} 114 | 115 | \item{grp_in}{vector of grouping objects for the biplot, must have the same number of observations as the original matrix used for the ordination} 116 | 117 | \item{cols}{chr string of optional colors for \code{grp_in}} 118 | 119 | \item{facet}{logical indicating if plot is faceted by groups in \code{grp_in}} 120 | 121 | \item{nfac}{numeric indicating number of columns if \code{facet = TRUE}} 122 | 123 | \item{addpts}{optional matrix or data.frame of additional points if constrained ordination is used (e.g., species locations in cca, rda)} 124 | 125 | \item{obslab}{logical if the row names for the observations in \code{obs} are plotted rather than points} 126 | 127 | \item{ptslab}{logical if the row names for the additional points (\code{addpts}) in constrained ordination are plotted as text} 128 | 129 | \item{ellipse}{logical if confidence ellipses are shown for each group, method from the ggbiplot package, at least one group must have more than two observations} 130 | 131 | \item{ellipse_pro}{numeric indicating confidence value for the ellipses} 132 | 133 | \item{poly}{logical if confidence ellipses are filled polygons, otherwise they are shown as empty ellipses} 134 | 135 | \item{polylntyp}{chr string for line type of polygon outlines if \code{poly = FALSE}, options are \code{twodash}, \code{solid}, \code{longdash}, \code{dotted}, \code{dotdash}, \code{dashed}, \code{blank}, or alternatively the grouping vector from \code{grp_in} can be used} 136 | 137 | \item{hull}{logical if convex hull is drawn around points or groups if provided} 138 | 139 | \item{arrow}{numeric indicating length of the arrow heads on the vectors, use \code{NULL} to suppress arrows} 140 | 141 | \item{labcol}{chr string for color of text labels on vectors} 142 | 143 | \item{veccol}{chr string for color of vectors} 144 | 145 | \item{vectyp}{chr string for line type of vectors, options are \code{twodash}, \code{solid}, \code{longdash}, \code{dotted}, \code{dotdash}, \code{dashed}, \code{blank}} 146 | 147 | \item{veclsz}{numeric for line size on vectors} 148 | 149 | \item{ext}{numeric indicating scalar distance of the labels from the arrow ends} 150 | 151 | \item{repel}{logical if overlapping text labels on vectors use \code{geom_text_repel} from the ggrepel package} 152 | 153 | \item{vec_ext}{numeric indicating a scalar extension for the ordination vectors} 154 | 155 | \item{vec_lab}{list of optional labels for vectors, defaults to names from input data. The input list must be named using the existing variables in the input data. Each element of the list will have the desired name change.} 156 | 157 | \item{size}{numeric indicating size of the observation points or a numeric vector equal in length to the rows in the input data} 158 | 159 | \item{sizelab}{chr string indicating an alternative legend title for size} 160 | 161 | \item{addsize}{numeric indicating size of the species points if addpts is not \code{NULL}} 162 | 163 | \item{addcol}{numeric indicating color of the species points if addpts is not \code{NULL}} 164 | 165 | \item{addpch}{numeric indicating point type of the species points if addpts is not \code{NULL}} 166 | 167 | \item{txt}{numeric indicating size of the text labels for the vectors, use \code{NULL} to suppress labels} 168 | 169 | \item{alpha}{numeric transparency of points and ellipses from 0 to 1} 170 | 171 | \item{alpha_el}{numeric transparency for confidence ellipses, also applies to filled convex hulls} 172 | 173 | \item{xlims}{two numeric values indicating x-axis limits} 174 | 175 | \item{ylims}{two numeric values indicating y-axis limits} 176 | 177 | \item{var_sub}{chr string indcating which labels to show. Regular expression matching is used.} 178 | 179 | \item{coord_fix}{logical indicating fixed, equal scaling for axes} 180 | 181 | \item{parse}{logical indicating if text labels are parsed} 182 | 183 | \item{grp_title}{chr string for legend title} 184 | 185 | \item{force}{numeric passed to \code{force} argument in \code{geom_text_repel} from the ggrepel package} 186 | 187 | \item{max.overlaps}{numeric passed to \code{max.overlaps} argument in \code{geom_text_repel} from the ggrepel package} 188 | 189 | \item{exp}{numeric of length two for expanding x and y axes, passed to \code{\link[ggplot2]{scale_y_continuous}} and \code{\link[ggplot2]{scale_y_continuous}}} 190 | 191 | \item{ord_in}{input ordination object} 192 | } 193 | \value{ 194 | A \code{\link[ggplot2]{ggplot}} object that can be further modified 195 | } 196 | \description{ 197 | Create an ordination biplot using ggplot2 including options for selecting axes, group color aesthetics, and selection of variables to plot. 198 | } 199 | \details{ 200 | Explained variance of axes for triplots are constrained values. 201 | } 202 | \examples{ 203 | 204 | library(ggplot2) 205 | 206 | # principal components analysis with the iris data set 207 | # prcomp 208 | ord <- prcomp(iris[, 1:4]) 209 | 210 | p <- ggord(ord, iris$Species) 211 | p 212 | 213 | p <- ggord(ord, iris$Species, cols = c('purple', 'orange', 'blue')) 214 | p 215 | 216 | p + scale_shape_manual('Groups', values = c(1, 2, 3)) 217 | p + theme_classic() 218 | p + theme(legend.position = 'top') 219 | 220 | # change the vector labels with vec_lab 221 | new_lab <- list(Sepal.Length = 'SL', Sepal.Width = 'SW', Petal.Width = 'PW', 222 | Petal.Length = 'PL') 223 | p <- ggord(ord, iris$Species, vec_lab = new_lab) 224 | p 225 | 226 | # faceted by group 227 | p <- ggord(ord, iris$Species, facet = TRUE, nfac = 3) 228 | p 229 | 230 | # principal components analysis with the iris dataset 231 | # princomp 232 | ord <- princomp(iris[, 1:4]) 233 | 234 | ggord(ord, iris$Species) 235 | 236 | # principal components analysis with the iris dataset 237 | # PCA 238 | library(FactoMineR) 239 | 240 | ord <- PCA(iris[, 1:4], graph = FALSE) 241 | 242 | ggord(ord, iris$Species) 243 | 244 | # principal components analysis with the iris dataset 245 | # dudi.pca 246 | library(ade4) 247 | 248 | ord <- dudi.pca(iris[, 1:4], scannf = FALSE, nf = 4) 249 | 250 | ggord(ord, iris$Species) 251 | 252 | # multiple correspondence analysis with the tea dataset 253 | # MCA 254 | data(tea, package = 'FactoMineR') 255 | tea <- tea[, c('Tea', 'sugar', 'price', 'age_Q', 'sex')] 256 | 257 | ord <- MCA(tea[, -1], graph = FALSE) 258 | 259 | ggord(ord, tea$Tea, parse = FALSE) # use parse = FALSE for labels with non alphanumeric characters 260 | 261 | # multiple correspondence analysis with the tea dataset 262 | # mca 263 | library(MASS) 264 | 265 | ord <- mca(tea[, -1]) 266 | 267 | ggord(ord, tea$Tea, parse = FALSE) # use parse = FALSE for labels with non alphanumeric characters 268 | 269 | # multiple correspondence analysis with the tea dataset 270 | # acm 271 | ord <- dudi.acm(tea[, -1], scannf = FALSE) 272 | 273 | ggord(ord, tea$Tea, parse = FALSE) # use parse = FALSE for labels with non alphanumeric characters 274 | 275 | # nonmetric multidimensional scaling with the iris dataset 276 | # metaMDS 277 | library(vegan) 278 | ord <- metaMDS(iris[, 1:4]) 279 | 280 | ggord(ord, iris$Species) 281 | 282 | # linear discriminant analysis 283 | # example from lda in MASS package 284 | ord <- lda(Species ~ ., iris, prior = rep(1, 3)/3) 285 | 286 | ggord(ord, iris$Species) 287 | 288 | # correspondence analysis 289 | # dudi.coa 290 | ord <- dudi.coa(iris[, 1:4], scannf = FALSE, nf = 4) 291 | 292 | ggord(ord, iris$Species) 293 | 294 | # correspondence analysis 295 | library(ca) 296 | ord <- ca(iris[, 1:4]) 297 | 298 | ggord(ord, iris$Species) 299 | 300 | # double principle coordinate analysis (DPCoA) 301 | library(ade4) 302 | data(ecomor) 303 | grp <- rep(c("Bu", "Ca", "Ch", "Pr"), each = 4) # sample groups 304 | dtaxo <- dist.taxo(ecomor$taxo) # taxonomic distance between species 305 | ord <- dpcoa(data.frame(t(ecomor$habitat)), dtaxo, scan = FALSE, nf = 2) 306 | 307 | ggord(ord, grp_in = grp, ellipse = FALSE, arrow = 0.2, txt = 3) 308 | 309 | # phylogenetic PCA 310 | # ppca 311 | 312 | library(adephylo) 313 | library(phylobase) 314 | library(ape) 315 | 316 | data(lizards) 317 | 318 | # example from help file, adephylo::ppca 319 | # original example from JOMBART ET AL 2010 320 | 321 | # build a tree and phylo4d object 322 | liz.tre <- read.tree(tex=lizards$hprA) 323 | liz.4d <- phylobase::phylo4d(liz.tre, lizards$traits) 324 | 325 | # remove duplicated populations 326 | liz.4d <- phylobase::prune(liz.4d, c(7,14)) 327 | 328 | # correct labels 329 | lab <- c("Pa", "Ph", "Ll", "Lmca", "Lmcy", "Phha", "Pha", 330 | "Pb", "Pm", "Ae", "Tt", "Ts", "Lviv", "La", "Ls", "Lvir") 331 | tipLabels(liz.4d) <- lab 332 | 333 | # remove size effect 334 | dat <- tdata(liz.4d, type="tip") 335 | dat <- log(dat) 336 | newdat <- data.frame(lapply(dat, function(v) residuals(lm(v~dat$mean.L)))) 337 | rownames(newdat) <- rownames(dat) 338 | tdata(liz.4d, type="tip") <- newdat[,-1] # replace data in the phylo4d object 339 | 340 | # create ppca 341 | liz.ppca <- ppca(liz.4d,scale=FALSE,scannf=FALSE,nfposi=1,nfnega=1, method="Abouheif") 342 | 343 | # plot 344 | ggord(liz.ppca) 345 | 346 | # distance-based redundancy analysis 347 | # dbrda from vegan 348 | data(varespec) 349 | data(varechem) 350 | 351 | ord <- dbrda(varespec ~ N + P + K + Condition(Al), varechem, dist = "bray") 352 | 353 | ggord(ord) 354 | 355 | ###### 356 | # triplots 357 | 358 | # redundancy analysis 359 | # rda from vegan 360 | ord <- rda(varespec, varechem) 361 | 362 | ggord(ord) 363 | 364 | # distance-based redundancy analysis 365 | # capscale from vegan 366 | ord <- capscale(varespec ~ N + P + K + Condition(Al), varechem, dist = "bray") 367 | 368 | ggord(ord) 369 | 370 | # canonical correspondence analysis 371 | # cca from vegan 372 | ord <- cca(varespec, varechem) 373 | 374 | ggord(ord) 375 | 376 | # species points as text 377 | # suppress site points 378 | ggord(ord, ptslab = TRUE, size = NA, addsize = 5, parse = TRUE) 379 | 380 | } 381 | \seealso{ 382 | \code{\link[ggplot2]{ggplot}} 383 | } 384 | -------------------------------------------------------------------------------- /README_files/bootstrap-3.3.1/css/bootstrap-theme.min.css: -------------------------------------------------------------------------------- 1 | /*! 2 | * Bootstrap v3.3.1 (http://getbootstrap.com) 3 | * Copyright 2011-2014 Twitter, Inc. 4 | * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) 5 | */.btn-default,.btn-primary,.btn-success,.btn-info,.btn-warning,.btn-danger{text-shadow:0 -1px 0 rgba(0,0,0,.2);-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.15),0 1px 1px rgba(0,0,0,.075);box-shadow:inset 0 1px 0 rgba(255,255,255,.15),0 1px 1px 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(https://github.com/twbs/bootstrap/blob/master/LICENSE) 5 | */ 6 | 7 | .btn-default, 8 | .btn-primary, 9 | .btn-success, 10 | .btn-info, 11 | .btn-warning, 12 | .btn-danger { 13 | text-shadow: 0 -1px 0 rgba(0, 0, 0, .2); 14 | -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 1px rgba(0, 0, 0, .075); 15 | box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 1px rgba(0, 0, 0, .075); 16 | } 17 | .btn-default:active, 18 | .btn-primary:active, 19 | .btn-success:active, 20 | .btn-info:active, 21 | .btn-warning:active, 22 | .btn-danger:active, 23 | .btn-default.active, 24 | .btn-primary.active, 25 | .btn-success.active, 26 | .btn-info.active, 27 | .btn-warning.active, 28 | .btn-danger.active { 29 | -webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125); 30 | box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125); 31 | } 32 | .btn-default .badge, 33 | .btn-primary .badge, 34 | .btn-success .badge, 35 | .btn-info .badge, 36 | .btn-warning .badge, 37 | .btn-danger .badge { 38 | text-shadow: none; 39 | } 40 | .btn:active, 41 | .btn.active { 42 | background-image: none; 43 | } 44 | .btn-default { 45 | text-shadow: 0 1px 0 #fff; 46 | background-image: -webkit-linear-gradient(top, #fff 0%, #e0e0e0 100%); 47 | background-image: -o-linear-gradient(top, #fff 0%, #e0e0e0 100%); 48 | background-image: -webkit-gradient(linear, left top, left bottom, from(#fff), to(#e0e0e0)); 49 | background-image: linear-gradient(to bottom, #fff 0%, #e0e0e0 100%); 50 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe0e0e0', GradientType=0); 51 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 52 | background-repeat: repeat-x; 53 | border-color: #dbdbdb; 54 | border-color: #ccc; 55 | } 56 | .btn-default:hover, 57 | .btn-default:focus { 58 | background-color: #e0e0e0; 59 | background-position: 0 -15px; 60 | } 61 | .btn-default:active, 62 | .btn-default.active { 63 | background-color: #e0e0e0; 64 | border-color: #dbdbdb; 65 | } 66 | .btn-default:disabled, 67 | .btn-default[disabled] { 68 | background-color: #e0e0e0; 69 | background-image: none; 70 | } 71 | .btn-primary { 72 | background-image: -webkit-linear-gradient(top, #337ab7 0%, #265a88 100%); 73 | background-image: -o-linear-gradient(top, #337ab7 0%, #265a88 100%); 74 | background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#265a88)); 75 | background-image: linear-gradient(to bottom, #337ab7 0%, #265a88 100%); 76 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff265a88', GradientType=0); 77 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 78 | background-repeat: repeat-x; 79 | border-color: #245580; 80 | } 81 | .btn-primary:hover, 82 | .btn-primary:focus { 83 | background-color: #265a88; 84 | background-position: 0 -15px; 85 | } 86 | .btn-primary:active, 87 | .btn-primary.active { 88 | background-color: #265a88; 89 | border-color: #245580; 90 | } 91 | .btn-primary:disabled, 92 | .btn-primary[disabled] { 93 | background-color: #265a88; 94 | background-image: none; 95 | } 96 | .btn-success { 97 | background-image: -webkit-linear-gradient(top, #5cb85c 0%, #419641 100%); 98 | background-image: -o-linear-gradient(top, #5cb85c 0%, #419641 100%); 99 | background-image: -webkit-gradient(linear, left top, left bottom, from(#5cb85c), to(#419641)); 100 | background-image: linear-gradient(to bottom, #5cb85c 0%, #419641 100%); 101 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5cb85c', endColorstr='#ff419641', GradientType=0); 102 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 103 | background-repeat: repeat-x; 104 | border-color: #3e8f3e; 105 | } 106 | .btn-success:hover, 107 | .btn-success:focus { 108 | background-color: #419641; 109 | background-position: 0 -15px; 110 | } 111 | .btn-success:active, 112 | .btn-success.active { 113 | background-color: #419641; 114 | border-color: #3e8f3e; 115 | } 116 | .btn-success:disabled, 117 | .btn-success[disabled] { 118 | background-color: #419641; 119 | background-image: none; 120 | } 121 | .btn-info { 122 | background-image: -webkit-linear-gradient(top, #5bc0de 0%, #2aabd2 100%); 123 | background-image: -o-linear-gradient(top, #5bc0de 0%, #2aabd2 100%); 124 | background-image: -webkit-gradient(linear, left top, left bottom, from(#5bc0de), to(#2aabd2)); 125 | background-image: linear-gradient(to bottom, #5bc0de 0%, #2aabd2 100%); 126 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff2aabd2', GradientType=0); 127 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 128 | background-repeat: repeat-x; 129 | border-color: #28a4c9; 130 | } 131 | .btn-info:hover, 132 | .btn-info:focus { 133 | background-color: #2aabd2; 134 | background-position: 0 -15px; 135 | } 136 | .btn-info:active, 137 | .btn-info.active { 138 | background-color: #2aabd2; 139 | border-color: #28a4c9; 140 | } 141 | .btn-info:disabled, 142 | .btn-info[disabled] { 143 | background-color: #2aabd2; 144 | background-image: none; 145 | } 146 | .btn-warning { 147 | background-image: -webkit-linear-gradient(top, #f0ad4e 0%, #eb9316 100%); 148 | background-image: -o-linear-gradient(top, #f0ad4e 0%, #eb9316 100%); 149 | background-image: -webkit-gradient(linear, left top, left bottom, from(#f0ad4e), to(#eb9316)); 150 | background-image: linear-gradient(to bottom, #f0ad4e 0%, #eb9316 100%); 151 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff0ad4e', endColorstr='#ffeb9316', GradientType=0); 152 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 153 | background-repeat: repeat-x; 154 | border-color: #e38d13; 155 | } 156 | .btn-warning:hover, 157 | .btn-warning:focus { 158 | background-color: #eb9316; 159 | background-position: 0 -15px; 160 | } 161 | .btn-warning:active, 162 | .btn-warning.active { 163 | background-color: #eb9316; 164 | border-color: #e38d13; 165 | } 166 | .btn-warning:disabled, 167 | .btn-warning[disabled] { 168 | background-color: #eb9316; 169 | background-image: none; 170 | } 171 | .btn-danger { 172 | background-image: -webkit-linear-gradient(top, #d9534f 0%, #c12e2a 100%); 173 | background-image: -o-linear-gradient(top, #d9534f 0%, #c12e2a 100%); 174 | background-image: -webkit-gradient(linear, left top, left bottom, from(#d9534f), to(#c12e2a)); 175 | background-image: linear-gradient(to bottom, #d9534f 0%, #c12e2a 100%); 176 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9534f', endColorstr='#ffc12e2a', GradientType=0); 177 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 178 | background-repeat: repeat-x; 179 | border-color: #b92c28; 180 | } 181 | .btn-danger:hover, 182 | .btn-danger:focus { 183 | background-color: #c12e2a; 184 | background-position: 0 -15px; 185 | } 186 | .btn-danger:active, 187 | .btn-danger.active { 188 | background-color: #c12e2a; 189 | border-color: #b92c28; 190 | } 191 | .btn-danger:disabled, 192 | .btn-danger[disabled] { 193 | background-color: #c12e2a; 194 | background-image: none; 195 | } 196 | .thumbnail, 197 | .img-thumbnail { 198 | -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .075); 199 | box-shadow: 0 1px 2px rgba(0, 0, 0, .075); 200 | } 201 | .dropdown-menu > li > a:hover, 202 | .dropdown-menu > li > a:focus { 203 | background-color: #e8e8e8; 204 | background-image: -webkit-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%); 205 | background-image: -o-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%); 206 | background-image: -webkit-gradient(linear, left top, left bottom, from(#f5f5f5), to(#e8e8e8)); 207 | background-image: linear-gradient(to bottom, #f5f5f5 0%, #e8e8e8 100%); 208 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#ffe8e8e8', GradientType=0); 209 | background-repeat: repeat-x; 210 | } 211 | .dropdown-menu > .active > a, 212 | .dropdown-menu > .active > a:hover, 213 | .dropdown-menu > .active > a:focus { 214 | background-color: #2e6da4; 215 | background-image: -webkit-linear-gradient(top, #337ab7 0%, #2e6da4 100%); 216 | background-image: -o-linear-gradient(top, #337ab7 0%, #2e6da4 100%); 217 | background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#2e6da4)); 218 | background-image: linear-gradient(to bottom, #337ab7 0%, #2e6da4 100%); 219 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2e6da4', GradientType=0); 220 | background-repeat: repeat-x; 221 | } 222 | .navbar-default { 223 | background-image: -webkit-linear-gradient(top, #fff 0%, #f8f8f8 100%); 224 | background-image: -o-linear-gradient(top, #fff 0%, #f8f8f8 100%); 225 | background-image: -webkit-gradient(linear, left top, left bottom, from(#fff), to(#f8f8f8)); 226 | background-image: linear-gradient(to bottom, #fff 0%, #f8f8f8 100%); 227 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#fff8f8f8', GradientType=0); 228 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 229 | background-repeat: repeat-x; 230 | border-radius: 4px; 231 | -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 5px rgba(0, 0, 0, .075); 232 | box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 5px rgba(0, 0, 0, .075); 233 | } 234 | .navbar-default .navbar-nav > .open > a, 235 | .navbar-default .navbar-nav > .active > a { 236 | background-image: -webkit-linear-gradient(top, #dbdbdb 0%, #e2e2e2 100%); 237 | background-image: -o-linear-gradient(top, #dbdbdb 0%, #e2e2e2 100%); 238 | background-image: -webkit-gradient(linear, left top, left bottom, from(#dbdbdb), to(#e2e2e2)); 239 | background-image: linear-gradient(to bottom, #dbdbdb 0%, #e2e2e2 100%); 240 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdbdbdb', endColorstr='#ffe2e2e2', GradientType=0); 241 | background-repeat: repeat-x; 242 | -webkit-box-shadow: inset 0 3px 9px rgba(0, 0, 0, .075); 243 | box-shadow: inset 0 3px 9px rgba(0, 0, 0, .075); 244 | } 245 | .navbar-brand, 246 | .navbar-nav > li > a { 247 | text-shadow: 0 1px 0 rgba(255, 255, 255, .25); 248 | } 249 | .navbar-inverse { 250 | background-image: -webkit-linear-gradient(top, #3c3c3c 0%, #222 100%); 251 | background-image: -o-linear-gradient(top, #3c3c3c 0%, #222 100%); 252 | background-image: -webkit-gradient(linear, left top, left bottom, from(#3c3c3c), to(#222)); 253 | background-image: linear-gradient(to bottom, #3c3c3c 0%, #222 100%); 254 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff3c3c3c', endColorstr='#ff222222', GradientType=0); 255 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 256 | background-repeat: repeat-x; 257 | } 258 | .navbar-inverse .navbar-nav > .open > a, 259 | .navbar-inverse .navbar-nav > .active > a { 260 | background-image: -webkit-linear-gradient(top, #080808 0%, #0f0f0f 100%); 261 | background-image: -o-linear-gradient(top, #080808 0%, #0f0f0f 100%); 262 | background-image: -webkit-gradient(linear, left top, left bottom, from(#080808), to(#0f0f0f)); 263 | background-image: linear-gradient(to bottom, #080808 0%, #0f0f0f 100%); 264 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff080808', endColorstr='#ff0f0f0f', GradientType=0); 265 | background-repeat: repeat-x; 266 | -webkit-box-shadow: inset 0 3px 9px rgba(0, 0, 0, .25); 267 | box-shadow: inset 0 3px 9px rgba(0, 0, 0, .25); 268 | } 269 | .navbar-inverse .navbar-brand, 270 | .navbar-inverse .navbar-nav > li > a { 271 | text-shadow: 0 -1px 0 rgba(0, 0, 0, .25); 272 | } 273 | .navbar-static-top, 274 | .navbar-fixed-top, 275 | .navbar-fixed-bottom { 276 | border-radius: 0; 277 | } 278 | @media (max-width: 767px) { 279 | .navbar .navbar-nav .open .dropdown-menu > .active > a, 280 | .navbar .navbar-nav .open .dropdown-menu > .active > a:hover, 281 | .navbar .navbar-nav .open .dropdown-menu > .active > a:focus { 282 | color: #fff; 283 | background-image: -webkit-linear-gradient(top, #337ab7 0%, #2e6da4 100%); 284 | background-image: -o-linear-gradient(top, #337ab7 0%, #2e6da4 100%); 285 | background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#2e6da4)); 286 | background-image: linear-gradient(to bottom, #337ab7 0%, #2e6da4 100%); 287 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2e6da4', GradientType=0); 288 | background-repeat: repeat-x; 289 | } 290 | } 291 | .alert { 292 | text-shadow: 0 1px 0 rgba(255, 255, 255, .2); 293 | -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .25), 0 1px 2px rgba(0, 0, 0, .05); 294 | box-shadow: inset 0 1px 0 rgba(255, 255, 255, .25), 0 1px 2px rgba(0, 0, 0, .05); 295 | } 296 | .alert-success { 297 | background-image: -webkit-linear-gradient(top, #dff0d8 0%, #c8e5bc 100%); 298 | background-image: -o-linear-gradient(top, #dff0d8 0%, #c8e5bc 100%); 299 | background-image: -webkit-gradient(linear, left top, left bottom, from(#dff0d8), to(#c8e5bc)); 300 | background-image: linear-gradient(to bottom, #dff0d8 0%, #c8e5bc 100%); 301 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdff0d8', endColorstr='#ffc8e5bc', GradientType=0); 302 | background-repeat: repeat-x; 303 | border-color: #b2dba1; 304 | } 305 | .alert-info { 306 | background-image: -webkit-linear-gradient(top, #d9edf7 0%, #b9def0 100%); 307 | background-image: -o-linear-gradient(top, #d9edf7 0%, #b9def0 100%); 308 | background-image: -webkit-gradient(linear, left top, left bottom, from(#d9edf7), to(#b9def0)); 309 | background-image: linear-gradient(to bottom, #d9edf7 0%, #b9def0 100%); 310 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9edf7', endColorstr='#ffb9def0', GradientType=0); 311 | background-repeat: repeat-x; 312 | border-color: #9acfea; 313 | } 314 | .alert-warning { 315 | background-image: -webkit-linear-gradient(top, #fcf8e3 0%, #f8efc0 100%); 316 | background-image: -o-linear-gradient(top, #fcf8e3 0%, #f8efc0 100%); 317 | background-image: -webkit-gradient(linear, left top, left bottom, from(#fcf8e3), to(#f8efc0)); 318 | background-image: linear-gradient(to bottom, #fcf8e3 0%, #f8efc0 100%); 319 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffcf8e3', endColorstr='#fff8efc0', GradientType=0); 320 | background-repeat: repeat-x; 321 | border-color: #f5e79e; 322 | } 323 | .alert-danger { 324 | background-image: -webkit-linear-gradient(top, #f2dede 0%, #e7c3c3 100%); 325 | background-image: -o-linear-gradient(top, #f2dede 0%, #e7c3c3 100%); 326 | background-image: -webkit-gradient(linear, left top, left bottom, from(#f2dede), to(#e7c3c3)); 327 | background-image: linear-gradient(to bottom, #f2dede 0%, #e7c3c3 100%); 328 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2dede', endColorstr='#ffe7c3c3', GradientType=0); 329 | background-repeat: repeat-x; 330 | border-color: #dca7a7; 331 | } 332 | .progress { 333 | background-image: -webkit-linear-gradient(top, #ebebeb 0%, #f5f5f5 100%); 334 | background-image: -o-linear-gradient(top, #ebebeb 0%, #f5f5f5 100%); 335 | background-image: -webkit-gradient(linear, left top, left bottom, from(#ebebeb), to(#f5f5f5)); 336 | background-image: linear-gradient(to bottom, #ebebeb 0%, #f5f5f5 100%); 337 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffebebeb', endColorstr='#fff5f5f5', GradientType=0); 338 | background-repeat: repeat-x; 339 | } 340 | .progress-bar { 341 | background-image: -webkit-linear-gradient(top, #337ab7 0%, #286090 100%); 342 | background-image: -o-linear-gradient(top, #337ab7 0%, #286090 100%); 343 | background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#286090)); 344 | background-image: linear-gradient(to bottom, #337ab7 0%, #286090 100%); 345 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff286090', GradientType=0); 346 | background-repeat: repeat-x; 347 | } 348 | .progress-bar-success { 349 | background-image: -webkit-linear-gradient(top, #5cb85c 0%, #449d44 100%); 350 | background-image: -o-linear-gradient(top, #5cb85c 0%, #449d44 100%); 351 | background-image: -webkit-gradient(linear, left top, left bottom, from(#5cb85c), to(#449d44)); 352 | background-image: linear-gradient(to bottom, #5cb85c 0%, #449d44 100%); 353 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5cb85c', endColorstr='#ff449d44', GradientType=0); 354 | background-repeat: repeat-x; 355 | } 356 | .progress-bar-info { 357 | background-image: -webkit-linear-gradient(top, #5bc0de 0%, #31b0d5 100%); 358 | background-image: -o-linear-gradient(top, #5bc0de 0%, #31b0d5 100%); 359 | background-image: -webkit-gradient(linear, left top, left bottom, from(#5bc0de), to(#31b0d5)); 360 | background-image: linear-gradient(to bottom, #5bc0de 0%, #31b0d5 100%); 361 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff31b0d5', GradientType=0); 362 | background-repeat: repeat-x; 363 | } 364 | .progress-bar-warning { 365 | background-image: -webkit-linear-gradient(top, #f0ad4e 0%, #ec971f 100%); 366 | background-image: -o-linear-gradient(top, #f0ad4e 0%, #ec971f 100%); 367 | background-image: -webkit-gradient(linear, left top, left bottom, from(#f0ad4e), to(#ec971f)); 368 | background-image: linear-gradient(to bottom, #f0ad4e 0%, #ec971f 100%); 369 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff0ad4e', endColorstr='#ffec971f', GradientType=0); 370 | background-repeat: repeat-x; 371 | } 372 | .progress-bar-danger { 373 | background-image: -webkit-linear-gradient(top, #d9534f 0%, #c9302c 100%); 374 | background-image: -o-linear-gradient(top, #d9534f 0%, #c9302c 100%); 375 | background-image: -webkit-gradient(linear, left top, left bottom, from(#d9534f), to(#c9302c)); 376 | background-image: linear-gradient(to bottom, #d9534f 0%, #c9302c 100%); 377 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9534f', endColorstr='#ffc9302c', GradientType=0); 378 | background-repeat: repeat-x; 379 | } 380 | .progress-bar-striped { 381 | background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); 382 | background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); 383 | background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); 384 | } 385 | .list-group { 386 | border-radius: 4px; 387 | -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .075); 388 | box-shadow: 0 1px 2px rgba(0, 0, 0, .075); 389 | } 390 | .list-group-item.active, 391 | .list-group-item.active:hover, 392 | .list-group-item.active:focus { 393 | text-shadow: 0 -1px 0 #286090; 394 | background-image: -webkit-linear-gradient(top, #337ab7 0%, #2b669a 100%); 395 | background-image: -o-linear-gradient(top, #337ab7 0%, #2b669a 100%); 396 | background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#2b669a)); 397 | background-image: linear-gradient(to bottom, #337ab7 0%, #2b669a 100%); 398 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2b669a', GradientType=0); 399 | background-repeat: repeat-x; 400 | border-color: #2b669a; 401 | } 402 | .list-group-item.active .badge, 403 | .list-group-item.active:hover .badge, 404 | .list-group-item.active:focus .badge { 405 | text-shadow: none; 406 | } 407 | .panel { 408 | -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .05); 409 | box-shadow: 0 1px 2px rgba(0, 0, 0, .05); 410 | } 411 | .panel-default > .panel-heading { 412 | background-image: -webkit-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%); 413 | background-image: -o-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%); 414 | background-image: -webkit-gradient(linear, left top, left bottom, from(#f5f5f5), to(#e8e8e8)); 415 | background-image: linear-gradient(to bottom, #f5f5f5 0%, #e8e8e8 100%); 416 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#ffe8e8e8', GradientType=0); 417 | background-repeat: repeat-x; 418 | } 419 | .panel-primary > .panel-heading { 420 | background-image: -webkit-linear-gradient(top, #337ab7 0%, #2e6da4 100%); 421 | background-image: -o-linear-gradient(top, #337ab7 0%, #2e6da4 100%); 422 | background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#2e6da4)); 423 | background-image: linear-gradient(to bottom, #337ab7 0%, #2e6da4 100%); 424 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2e6da4', GradientType=0); 425 | background-repeat: repeat-x; 426 | } 427 | .panel-success > .panel-heading { 428 | background-image: -webkit-linear-gradient(top, #dff0d8 0%, #d0e9c6 100%); 429 | background-image: -o-linear-gradient(top, #dff0d8 0%, #d0e9c6 100%); 430 | background-image: -webkit-gradient(linear, left top, left bottom, from(#dff0d8), to(#d0e9c6)); 431 | background-image: linear-gradient(to bottom, #dff0d8 0%, #d0e9c6 100%); 432 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdff0d8', endColorstr='#ffd0e9c6', GradientType=0); 433 | background-repeat: repeat-x; 434 | } 435 | .panel-info > .panel-heading { 436 | background-image: -webkit-linear-gradient(top, #d9edf7 0%, #c4e3f3 100%); 437 | background-image: -o-linear-gradient(top, #d9edf7 0%, #c4e3f3 100%); 438 | background-image: -webkit-gradient(linear, left top, left bottom, from(#d9edf7), to(#c4e3f3)); 439 | background-image: linear-gradient(to bottom, #d9edf7 0%, #c4e3f3 100%); 440 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9edf7', endColorstr='#ffc4e3f3', GradientType=0); 441 | background-repeat: repeat-x; 442 | } 443 | .panel-warning > .panel-heading { 444 | background-image: -webkit-linear-gradient(top, #fcf8e3 0%, #faf2cc 100%); 445 | background-image: -o-linear-gradient(top, #fcf8e3 0%, #faf2cc 100%); 446 | background-image: -webkit-gradient(linear, left top, left bottom, from(#fcf8e3), to(#faf2cc)); 447 | background-image: linear-gradient(to bottom, #fcf8e3 0%, #faf2cc 100%); 448 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffcf8e3', endColorstr='#fffaf2cc', GradientType=0); 449 | background-repeat: repeat-x; 450 | } 451 | .panel-danger > .panel-heading { 452 | background-image: -webkit-linear-gradient(top, #f2dede 0%, #ebcccc 100%); 453 | background-image: -o-linear-gradient(top, #f2dede 0%, #ebcccc 100%); 454 | background-image: -webkit-gradient(linear, left top, left bottom, from(#f2dede), to(#ebcccc)); 455 | background-image: linear-gradient(to bottom, #f2dede 0%, #ebcccc 100%); 456 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2dede', endColorstr='#ffebcccc', GradientType=0); 457 | background-repeat: repeat-x; 458 | } 459 | .well { 460 | background-image: -webkit-linear-gradient(top, #e8e8e8 0%, #f5f5f5 100%); 461 | background-image: -o-linear-gradient(top, #e8e8e8 0%, #f5f5f5 100%); 462 | background-image: -webkit-gradient(linear, left top, left bottom, from(#e8e8e8), to(#f5f5f5)); 463 | background-image: linear-gradient(to bottom, #e8e8e8 0%, #f5f5f5 100%); 464 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffe8e8e8', endColorstr='#fff5f5f5', GradientType=0); 465 | background-repeat: repeat-x; 466 | border-color: #dcdcdc; 467 | -webkit-box-shadow: inset 0 1px 3px rgba(0, 0, 0, .05), 0 1px 0 rgba(255, 255, 255, .1); 468 | box-shadow: inset 0 1px 3px rgba(0, 0, 0, .05), 0 1px 0 rgba(255, 255, 255, .1); 469 | } 470 | /*# sourceMappingURL=bootstrap-theme.css.map */ 471 | -------------------------------------------------------------------------------- /README_files/bootstrap-3.3.5/css/bootstrap-theme.css: -------------------------------------------------------------------------------- 1 | /*! 2 | * Bootstrap v3.3.5 (http://getbootstrap.com) 3 | * Copyright 2011-2015 Twitter, Inc. 4 | * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) 5 | */ 6 | .btn-default, 7 | .btn-primary, 8 | .btn-success, 9 | .btn-info, 10 | .btn-warning, 11 | .btn-danger { 12 | text-shadow: 0 -1px 0 rgba(0, 0, 0, .2); 13 | -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 1px rgba(0, 0, 0, .075); 14 | box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 1px rgba(0, 0, 0, .075); 15 | } 16 | .btn-default:active, 17 | .btn-primary:active, 18 | .btn-success:active, 19 | .btn-info:active, 20 | .btn-warning:active, 21 | .btn-danger:active, 22 | .btn-default.active, 23 | .btn-primary.active, 24 | .btn-success.active, 25 | .btn-info.active, 26 | .btn-warning.active, 27 | .btn-danger.active { 28 | -webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125); 29 | box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125); 30 | } 31 | .btn-default.disabled, 32 | .btn-primary.disabled, 33 | .btn-success.disabled, 34 | .btn-info.disabled, 35 | .btn-warning.disabled, 36 | .btn-danger.disabled, 37 | .btn-default[disabled], 38 | .btn-primary[disabled], 39 | .btn-success[disabled], 40 | .btn-info[disabled], 41 | .btn-warning[disabled], 42 | .btn-danger[disabled], 43 | fieldset[disabled] .btn-default, 44 | fieldset[disabled] .btn-primary, 45 | fieldset[disabled] .btn-success, 46 | fieldset[disabled] .btn-info, 47 | fieldset[disabled] .btn-warning, 48 | fieldset[disabled] .btn-danger { 49 | -webkit-box-shadow: none; 50 | box-shadow: none; 51 | } 52 | .btn-default .badge, 53 | .btn-primary .badge, 54 | .btn-success .badge, 55 | .btn-info .badge, 56 | .btn-warning .badge, 57 | .btn-danger .badge { 58 | text-shadow: none; 59 | } 60 | .btn:active, 61 | .btn.active { 62 | background-image: none; 63 | } 64 | .btn-default { 65 | text-shadow: 0 1px 0 #fff; 66 | background-image: -webkit-linear-gradient(top, #fff 0%, #e0e0e0 100%); 67 | background-image: -o-linear-gradient(top, #fff 0%, #e0e0e0 100%); 68 | background-image: -webkit-gradient(linear, left top, left bottom, from(#fff), to(#e0e0e0)); 69 | background-image: linear-gradient(to bottom, #fff 0%, #e0e0e0 100%); 70 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe0e0e0', GradientType=0); 71 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 72 | background-repeat: repeat-x; 73 | border-color: #dbdbdb; 74 | border-color: #ccc; 75 | } 76 | .btn-default:hover, 77 | .btn-default:focus { 78 | background-color: #e0e0e0; 79 | background-position: 0 -15px; 80 | } 81 | .btn-default:active, 82 | .btn-default.active { 83 | background-color: #e0e0e0; 84 | border-color: #dbdbdb; 85 | } 86 | .btn-default.disabled, 87 | .btn-default[disabled], 88 | fieldset[disabled] .btn-default, 89 | .btn-default.disabled:hover, 90 | .btn-default[disabled]:hover, 91 | fieldset[disabled] .btn-default:hover, 92 | .btn-default.disabled:focus, 93 | .btn-default[disabled]:focus, 94 | fieldset[disabled] .btn-default:focus, 95 | .btn-default.disabled.focus, 96 | .btn-default[disabled].focus, 97 | fieldset[disabled] .btn-default.focus, 98 | .btn-default.disabled:active, 99 | .btn-default[disabled]:active, 100 | fieldset[disabled] .btn-default:active, 101 | .btn-default.disabled.active, 102 | .btn-default[disabled].active, 103 | fieldset[disabled] .btn-default.active { 104 | background-color: #e0e0e0; 105 | background-image: none; 106 | } 107 | .btn-primary { 108 | background-image: -webkit-linear-gradient(top, #337ab7 0%, #265a88 100%); 109 | background-image: -o-linear-gradient(top, #337ab7 0%, #265a88 100%); 110 | background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#265a88)); 111 | background-image: linear-gradient(to bottom, #337ab7 0%, #265a88 100%); 112 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff265a88', GradientType=0); 113 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 114 | background-repeat: repeat-x; 115 | border-color: #245580; 116 | } 117 | .btn-primary:hover, 118 | .btn-primary:focus { 119 | background-color: #265a88; 120 | background-position: 0 -15px; 121 | } 122 | .btn-primary:active, 123 | .btn-primary.active { 124 | background-color: #265a88; 125 | border-color: #245580; 126 | } 127 | .btn-primary.disabled, 128 | .btn-primary[disabled], 129 | fieldset[disabled] .btn-primary, 130 | .btn-primary.disabled:hover, 131 | .btn-primary[disabled]:hover, 132 | fieldset[disabled] .btn-primary:hover, 133 | .btn-primary.disabled:focus, 134 | .btn-primary[disabled]:focus, 135 | fieldset[disabled] .btn-primary:focus, 136 | .btn-primary.disabled.focus, 137 | .btn-primary[disabled].focus, 138 | fieldset[disabled] .btn-primary.focus, 139 | .btn-primary.disabled:active, 140 | .btn-primary[disabled]:active, 141 | fieldset[disabled] .btn-primary:active, 142 | .btn-primary.disabled.active, 143 | .btn-primary[disabled].active, 144 | fieldset[disabled] .btn-primary.active { 145 | background-color: #265a88; 146 | background-image: none; 147 | } 148 | .btn-success { 149 | background-image: -webkit-linear-gradient(top, #5cb85c 0%, #419641 100%); 150 | background-image: -o-linear-gradient(top, #5cb85c 0%, #419641 100%); 151 | background-image: -webkit-gradient(linear, left top, left bottom, from(#5cb85c), to(#419641)); 152 | background-image: linear-gradient(to bottom, #5cb85c 0%, #419641 100%); 153 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5cb85c', endColorstr='#ff419641', GradientType=0); 154 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 155 | background-repeat: repeat-x; 156 | border-color: #3e8f3e; 157 | } 158 | .btn-success:hover, 159 | .btn-success:focus { 160 | background-color: #419641; 161 | background-position: 0 -15px; 162 | } 163 | .btn-success:active, 164 | .btn-success.active { 165 | background-color: #419641; 166 | border-color: #3e8f3e; 167 | } 168 | .btn-success.disabled, 169 | .btn-success[disabled], 170 | fieldset[disabled] .btn-success, 171 | .btn-success.disabled:hover, 172 | .btn-success[disabled]:hover, 173 | fieldset[disabled] .btn-success:hover, 174 | .btn-success.disabled:focus, 175 | .btn-success[disabled]:focus, 176 | fieldset[disabled] .btn-success:focus, 177 | .btn-success.disabled.focus, 178 | .btn-success[disabled].focus, 179 | fieldset[disabled] .btn-success.focus, 180 | .btn-success.disabled:active, 181 | .btn-success[disabled]:active, 182 | fieldset[disabled] .btn-success:active, 183 | .btn-success.disabled.active, 184 | .btn-success[disabled].active, 185 | fieldset[disabled] .btn-success.active { 186 | background-color: #419641; 187 | background-image: none; 188 | } 189 | .btn-info { 190 | background-image: -webkit-linear-gradient(top, #5bc0de 0%, #2aabd2 100%); 191 | background-image: -o-linear-gradient(top, #5bc0de 0%, #2aabd2 100%); 192 | background-image: -webkit-gradient(linear, left top, left bottom, from(#5bc0de), to(#2aabd2)); 193 | background-image: linear-gradient(to bottom, #5bc0de 0%, #2aabd2 100%); 194 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff2aabd2', GradientType=0); 195 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 196 | background-repeat: repeat-x; 197 | border-color: #28a4c9; 198 | } 199 | .btn-info:hover, 200 | .btn-info:focus { 201 | background-color: #2aabd2; 202 | background-position: 0 -15px; 203 | } 204 | .btn-info:active, 205 | .btn-info.active { 206 | background-color: #2aabd2; 207 | border-color: #28a4c9; 208 | } 209 | .btn-info.disabled, 210 | .btn-info[disabled], 211 | fieldset[disabled] .btn-info, 212 | .btn-info.disabled:hover, 213 | .btn-info[disabled]:hover, 214 | fieldset[disabled] .btn-info:hover, 215 | .btn-info.disabled:focus, 216 | .btn-info[disabled]:focus, 217 | fieldset[disabled] .btn-info:focus, 218 | .btn-info.disabled.focus, 219 | .btn-info[disabled].focus, 220 | fieldset[disabled] .btn-info.focus, 221 | .btn-info.disabled:active, 222 | .btn-info[disabled]:active, 223 | fieldset[disabled] .btn-info:active, 224 | .btn-info.disabled.active, 225 | .btn-info[disabled].active, 226 | fieldset[disabled] .btn-info.active { 227 | background-color: #2aabd2; 228 | background-image: none; 229 | } 230 | .btn-warning { 231 | background-image: -webkit-linear-gradient(top, #f0ad4e 0%, #eb9316 100%); 232 | background-image: -o-linear-gradient(top, #f0ad4e 0%, #eb9316 100%); 233 | background-image: -webkit-gradient(linear, left top, left bottom, from(#f0ad4e), to(#eb9316)); 234 | background-image: linear-gradient(to bottom, #f0ad4e 0%, #eb9316 100%); 235 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff0ad4e', endColorstr='#ffeb9316', GradientType=0); 236 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 237 | background-repeat: repeat-x; 238 | border-color: #e38d13; 239 | } 240 | .btn-warning:hover, 241 | .btn-warning:focus { 242 | background-color: #eb9316; 243 | background-position: 0 -15px; 244 | } 245 | .btn-warning:active, 246 | .btn-warning.active { 247 | background-color: #eb9316; 248 | border-color: #e38d13; 249 | } 250 | .btn-warning.disabled, 251 | .btn-warning[disabled], 252 | fieldset[disabled] .btn-warning, 253 | .btn-warning.disabled:hover, 254 | .btn-warning[disabled]:hover, 255 | fieldset[disabled] .btn-warning:hover, 256 | .btn-warning.disabled:focus, 257 | .btn-warning[disabled]:focus, 258 | fieldset[disabled] .btn-warning:focus, 259 | .btn-warning.disabled.focus, 260 | .btn-warning[disabled].focus, 261 | fieldset[disabled] .btn-warning.focus, 262 | .btn-warning.disabled:active, 263 | .btn-warning[disabled]:active, 264 | fieldset[disabled] .btn-warning:active, 265 | .btn-warning.disabled.active, 266 | .btn-warning[disabled].active, 267 | fieldset[disabled] .btn-warning.active { 268 | background-color: #eb9316; 269 | background-image: none; 270 | } 271 | .btn-danger { 272 | background-image: -webkit-linear-gradient(top, #d9534f 0%, #c12e2a 100%); 273 | background-image: -o-linear-gradient(top, #d9534f 0%, #c12e2a 100%); 274 | background-image: -webkit-gradient(linear, left top, left bottom, from(#d9534f), to(#c12e2a)); 275 | background-image: linear-gradient(to bottom, #d9534f 0%, #c12e2a 100%); 276 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9534f', endColorstr='#ffc12e2a', GradientType=0); 277 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 278 | background-repeat: repeat-x; 279 | border-color: #b92c28; 280 | } 281 | .btn-danger:hover, 282 | .btn-danger:focus { 283 | background-color: #c12e2a; 284 | background-position: 0 -15px; 285 | } 286 | .btn-danger:active, 287 | .btn-danger.active { 288 | background-color: #c12e2a; 289 | border-color: #b92c28; 290 | } 291 | .btn-danger.disabled, 292 | .btn-danger[disabled], 293 | fieldset[disabled] .btn-danger, 294 | .btn-danger.disabled:hover, 295 | .btn-danger[disabled]:hover, 296 | fieldset[disabled] .btn-danger:hover, 297 | .btn-danger.disabled:focus, 298 | .btn-danger[disabled]:focus, 299 | fieldset[disabled] .btn-danger:focus, 300 | .btn-danger.disabled.focus, 301 | .btn-danger[disabled].focus, 302 | fieldset[disabled] .btn-danger.focus, 303 | .btn-danger.disabled:active, 304 | .btn-danger[disabled]:active, 305 | fieldset[disabled] .btn-danger:active, 306 | .btn-danger.disabled.active, 307 | .btn-danger[disabled].active, 308 | fieldset[disabled] .btn-danger.active { 309 | background-color: #c12e2a; 310 | background-image: none; 311 | } 312 | .thumbnail, 313 | .img-thumbnail { 314 | -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .075); 315 | box-shadow: 0 1px 2px rgba(0, 0, 0, .075); 316 | } 317 | .dropdown-menu > li > a:hover, 318 | .dropdown-menu > li > a:focus { 319 | background-color: #e8e8e8; 320 | background-image: -webkit-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%); 321 | background-image: -o-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%); 322 | background-image: -webkit-gradient(linear, left top, left bottom, from(#f5f5f5), to(#e8e8e8)); 323 | background-image: linear-gradient(to bottom, #f5f5f5 0%, #e8e8e8 100%); 324 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#ffe8e8e8', GradientType=0); 325 | background-repeat: repeat-x; 326 | } 327 | .dropdown-menu > .active > a, 328 | .dropdown-menu > .active > a:hover, 329 | .dropdown-menu > .active > a:focus { 330 | background-color: #2e6da4; 331 | background-image: -webkit-linear-gradient(top, #337ab7 0%, #2e6da4 100%); 332 | background-image: -o-linear-gradient(top, #337ab7 0%, #2e6da4 100%); 333 | background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#2e6da4)); 334 | background-image: linear-gradient(to bottom, #337ab7 0%, #2e6da4 100%); 335 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2e6da4', GradientType=0); 336 | background-repeat: repeat-x; 337 | } 338 | .navbar-default { 339 | background-image: -webkit-linear-gradient(top, #fff 0%, #f8f8f8 100%); 340 | background-image: -o-linear-gradient(top, #fff 0%, #f8f8f8 100%); 341 | background-image: -webkit-gradient(linear, left top, left bottom, from(#fff), to(#f8f8f8)); 342 | background-image: linear-gradient(to bottom, #fff 0%, #f8f8f8 100%); 343 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#fff8f8f8', GradientType=0); 344 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 345 | background-repeat: repeat-x; 346 | border-radius: 4px; 347 | -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 5px rgba(0, 0, 0, .075); 348 | box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 5px rgba(0, 0, 0, .075); 349 | } 350 | .navbar-default .navbar-nav > .open > a, 351 | .navbar-default .navbar-nav > .active > a { 352 | background-image: -webkit-linear-gradient(top, #dbdbdb 0%, #e2e2e2 100%); 353 | background-image: -o-linear-gradient(top, #dbdbdb 0%, #e2e2e2 100%); 354 | background-image: -webkit-gradient(linear, left top, left bottom, from(#dbdbdb), to(#e2e2e2)); 355 | background-image: linear-gradient(to bottom, #dbdbdb 0%, #e2e2e2 100%); 356 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdbdbdb', endColorstr='#ffe2e2e2', GradientType=0); 357 | background-repeat: repeat-x; 358 | -webkit-box-shadow: inset 0 3px 9px rgba(0, 0, 0, .075); 359 | box-shadow: inset 0 3px 9px rgba(0, 0, 0, .075); 360 | } 361 | .navbar-brand, 362 | .navbar-nav > li > a { 363 | text-shadow: 0 1px 0 rgba(255, 255, 255, .25); 364 | } 365 | .navbar-inverse { 366 | background-image: -webkit-linear-gradient(top, #3c3c3c 0%, #222 100%); 367 | background-image: -o-linear-gradient(top, #3c3c3c 0%, #222 100%); 368 | background-image: -webkit-gradient(linear, left top, left bottom, from(#3c3c3c), to(#222)); 369 | background-image: linear-gradient(to bottom, #3c3c3c 0%, #222 100%); 370 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff3c3c3c', endColorstr='#ff222222', GradientType=0); 371 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 372 | background-repeat: repeat-x; 373 | border-radius: 4px; 374 | } 375 | .navbar-inverse .navbar-nav > .open > a, 376 | .navbar-inverse .navbar-nav > .active > a { 377 | background-image: -webkit-linear-gradient(top, #080808 0%, #0f0f0f 100%); 378 | background-image: -o-linear-gradient(top, #080808 0%, #0f0f0f 100%); 379 | background-image: -webkit-gradient(linear, left top, left bottom, from(#080808), to(#0f0f0f)); 380 | background-image: linear-gradient(to bottom, #080808 0%, #0f0f0f 100%); 381 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff080808', endColorstr='#ff0f0f0f', GradientType=0); 382 | background-repeat: repeat-x; 383 | -webkit-box-shadow: inset 0 3px 9px rgba(0, 0, 0, .25); 384 | box-shadow: inset 0 3px 9px rgba(0, 0, 0, .25); 385 | } 386 | .navbar-inverse .navbar-brand, 387 | .navbar-inverse .navbar-nav > li > a { 388 | text-shadow: 0 -1px 0 rgba(0, 0, 0, .25); 389 | } 390 | .navbar-static-top, 391 | .navbar-fixed-top, 392 | .navbar-fixed-bottom { 393 | border-radius: 0; 394 | } 395 | @media (max-width: 767px) { 396 | .navbar .navbar-nav .open .dropdown-menu > .active > a, 397 | .navbar .navbar-nav .open .dropdown-menu > .active > a:hover, 398 | .navbar .navbar-nav .open .dropdown-menu > .active > a:focus { 399 | color: #fff; 400 | background-image: -webkit-linear-gradient(top, #337ab7 0%, #2e6da4 100%); 401 | background-image: -o-linear-gradient(top, #337ab7 0%, #2e6da4 100%); 402 | background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#2e6da4)); 403 | background-image: linear-gradient(to bottom, #337ab7 0%, #2e6da4 100%); 404 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2e6da4', GradientType=0); 405 | background-repeat: repeat-x; 406 | } 407 | } 408 | .alert { 409 | text-shadow: 0 1px 0 rgba(255, 255, 255, .2); 410 | -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .25), 0 1px 2px rgba(0, 0, 0, .05); 411 | box-shadow: inset 0 1px 0 rgba(255, 255, 255, .25), 0 1px 2px rgba(0, 0, 0, .05); 412 | } 413 | .alert-success { 414 | background-image: -webkit-linear-gradient(top, #dff0d8 0%, #c8e5bc 100%); 415 | background-image: -o-linear-gradient(top, #dff0d8 0%, #c8e5bc 100%); 416 | background-image: -webkit-gradient(linear, left top, left bottom, from(#dff0d8), to(#c8e5bc)); 417 | background-image: linear-gradient(to bottom, #dff0d8 0%, #c8e5bc 100%); 418 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdff0d8', endColorstr='#ffc8e5bc', GradientType=0); 419 | background-repeat: repeat-x; 420 | border-color: #b2dba1; 421 | } 422 | .alert-info { 423 | background-image: -webkit-linear-gradient(top, #d9edf7 0%, #b9def0 100%); 424 | background-image: -o-linear-gradient(top, #d9edf7 0%, #b9def0 100%); 425 | background-image: -webkit-gradient(linear, left top, left bottom, from(#d9edf7), to(#b9def0)); 426 | background-image: linear-gradient(to bottom, #d9edf7 0%, #b9def0 100%); 427 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9edf7', endColorstr='#ffb9def0', GradientType=0); 428 | background-repeat: repeat-x; 429 | border-color: #9acfea; 430 | } 431 | .alert-warning { 432 | background-image: -webkit-linear-gradient(top, #fcf8e3 0%, #f8efc0 100%); 433 | background-image: -o-linear-gradient(top, #fcf8e3 0%, #f8efc0 100%); 434 | background-image: -webkit-gradient(linear, left top, left bottom, from(#fcf8e3), to(#f8efc0)); 435 | background-image: linear-gradient(to bottom, #fcf8e3 0%, #f8efc0 100%); 436 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffcf8e3', endColorstr='#fff8efc0', GradientType=0); 437 | background-repeat: repeat-x; 438 | border-color: #f5e79e; 439 | } 440 | .alert-danger { 441 | background-image: -webkit-linear-gradient(top, #f2dede 0%, #e7c3c3 100%); 442 | background-image: -o-linear-gradient(top, #f2dede 0%, #e7c3c3 100%); 443 | background-image: -webkit-gradient(linear, left top, left bottom, from(#f2dede), to(#e7c3c3)); 444 | background-image: linear-gradient(to bottom, #f2dede 0%, #e7c3c3 100%); 445 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2dede', endColorstr='#ffe7c3c3', GradientType=0); 446 | background-repeat: repeat-x; 447 | border-color: #dca7a7; 448 | } 449 | .progress { 450 | background-image: -webkit-linear-gradient(top, #ebebeb 0%, #f5f5f5 100%); 451 | background-image: -o-linear-gradient(top, #ebebeb 0%, #f5f5f5 100%); 452 | background-image: -webkit-gradient(linear, left top, left bottom, from(#ebebeb), to(#f5f5f5)); 453 | background-image: linear-gradient(to bottom, #ebebeb 0%, #f5f5f5 100%); 454 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffebebeb', endColorstr='#fff5f5f5', GradientType=0); 455 | background-repeat: repeat-x; 456 | } 457 | .progress-bar { 458 | background-image: -webkit-linear-gradient(top, #337ab7 0%, #286090 100%); 459 | background-image: -o-linear-gradient(top, #337ab7 0%, #286090 100%); 460 | background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#286090)); 461 | background-image: linear-gradient(to bottom, #337ab7 0%, #286090 100%); 462 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff286090', GradientType=0); 463 | background-repeat: repeat-x; 464 | } 465 | .progress-bar-success { 466 | background-image: -webkit-linear-gradient(top, #5cb85c 0%, #449d44 100%); 467 | background-image: -o-linear-gradient(top, #5cb85c 0%, #449d44 100%); 468 | background-image: -webkit-gradient(linear, left top, left bottom, from(#5cb85c), to(#449d44)); 469 | background-image: linear-gradient(to bottom, #5cb85c 0%, #449d44 100%); 470 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5cb85c', endColorstr='#ff449d44', GradientType=0); 471 | background-repeat: repeat-x; 472 | } 473 | .progress-bar-info { 474 | background-image: -webkit-linear-gradient(top, #5bc0de 0%, #31b0d5 100%); 475 | background-image: -o-linear-gradient(top, #5bc0de 0%, #31b0d5 100%); 476 | background-image: -webkit-gradient(linear, left top, left bottom, from(#5bc0de), to(#31b0d5)); 477 | background-image: linear-gradient(to bottom, #5bc0de 0%, #31b0d5 100%); 478 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff31b0d5', GradientType=0); 479 | background-repeat: repeat-x; 480 | } 481 | .progress-bar-warning { 482 | background-image: -webkit-linear-gradient(top, #f0ad4e 0%, #ec971f 100%); 483 | background-image: -o-linear-gradient(top, #f0ad4e 0%, #ec971f 100%); 484 | background-image: -webkit-gradient(linear, left top, left bottom, from(#f0ad4e), to(#ec971f)); 485 | background-image: linear-gradient(to bottom, #f0ad4e 0%, #ec971f 100%); 486 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff0ad4e', endColorstr='#ffec971f', GradientType=0); 487 | background-repeat: repeat-x; 488 | } 489 | .progress-bar-danger { 490 | background-image: -webkit-linear-gradient(top, #d9534f 0%, #c9302c 100%); 491 | background-image: -o-linear-gradient(top, #d9534f 0%, #c9302c 100%); 492 | background-image: -webkit-gradient(linear, left top, left bottom, from(#d9534f), to(#c9302c)); 493 | background-image: linear-gradient(to bottom, #d9534f 0%, #c9302c 100%); 494 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9534f', endColorstr='#ffc9302c', GradientType=0); 495 | background-repeat: repeat-x; 496 | } 497 | .progress-bar-striped { 498 | background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); 499 | background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); 500 | background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent); 501 | } 502 | .list-group { 503 | border-radius: 4px; 504 | -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .075); 505 | box-shadow: 0 1px 2px rgba(0, 0, 0, .075); 506 | } 507 | .list-group-item.active, 508 | .list-group-item.active:hover, 509 | .list-group-item.active:focus { 510 | text-shadow: 0 -1px 0 #286090; 511 | background-image: -webkit-linear-gradient(top, #337ab7 0%, #2b669a 100%); 512 | background-image: -o-linear-gradient(top, #337ab7 0%, #2b669a 100%); 513 | background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#2b669a)); 514 | background-image: linear-gradient(to bottom, #337ab7 0%, #2b669a 100%); 515 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2b669a', GradientType=0); 516 | background-repeat: repeat-x; 517 | border-color: #2b669a; 518 | } 519 | .list-group-item.active .badge, 520 | .list-group-item.active:hover .badge, 521 | .list-group-item.active:focus .badge { 522 | text-shadow: none; 523 | } 524 | .panel { 525 | -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .05); 526 | box-shadow: 0 1px 2px rgba(0, 0, 0, .05); 527 | } 528 | .panel-default > .panel-heading { 529 | background-image: -webkit-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%); 530 | background-image: -o-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%); 531 | background-image: -webkit-gradient(linear, left top, left bottom, from(#f5f5f5), to(#e8e8e8)); 532 | background-image: linear-gradient(to bottom, #f5f5f5 0%, #e8e8e8 100%); 533 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#ffe8e8e8', GradientType=0); 534 | background-repeat: repeat-x; 535 | } 536 | .panel-primary > .panel-heading { 537 | background-image: -webkit-linear-gradient(top, #337ab7 0%, #2e6da4 100%); 538 | background-image: -o-linear-gradient(top, #337ab7 0%, #2e6da4 100%); 539 | background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#2e6da4)); 540 | background-image: linear-gradient(to bottom, #337ab7 0%, #2e6da4 100%); 541 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2e6da4', GradientType=0); 542 | background-repeat: repeat-x; 543 | } 544 | .panel-success > .panel-heading { 545 | background-image: -webkit-linear-gradient(top, #dff0d8 0%, #d0e9c6 100%); 546 | background-image: -o-linear-gradient(top, #dff0d8 0%, #d0e9c6 100%); 547 | background-image: -webkit-gradient(linear, left top, left bottom, from(#dff0d8), to(#d0e9c6)); 548 | background-image: linear-gradient(to bottom, #dff0d8 0%, #d0e9c6 100%); 549 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdff0d8', endColorstr='#ffd0e9c6', GradientType=0); 550 | background-repeat: repeat-x; 551 | } 552 | .panel-info > .panel-heading { 553 | background-image: -webkit-linear-gradient(top, #d9edf7 0%, #c4e3f3 100%); 554 | background-image: -o-linear-gradient(top, #d9edf7 0%, #c4e3f3 100%); 555 | background-image: -webkit-gradient(linear, left top, left bottom, from(#d9edf7), to(#c4e3f3)); 556 | background-image: linear-gradient(to bottom, #d9edf7 0%, #c4e3f3 100%); 557 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9edf7', endColorstr='#ffc4e3f3', GradientType=0); 558 | background-repeat: repeat-x; 559 | } 560 | .panel-warning > .panel-heading { 561 | background-image: -webkit-linear-gradient(top, #fcf8e3 0%, #faf2cc 100%); 562 | background-image: -o-linear-gradient(top, #fcf8e3 0%, #faf2cc 100%); 563 | background-image: -webkit-gradient(linear, left top, left bottom, from(#fcf8e3), to(#faf2cc)); 564 | background-image: linear-gradient(to bottom, #fcf8e3 0%, #faf2cc 100%); 565 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffcf8e3', endColorstr='#fffaf2cc', GradientType=0); 566 | background-repeat: repeat-x; 567 | } 568 | .panel-danger > .panel-heading { 569 | background-image: -webkit-linear-gradient(top, #f2dede 0%, #ebcccc 100%); 570 | background-image: -o-linear-gradient(top, #f2dede 0%, #ebcccc 100%); 571 | background-image: -webkit-gradient(linear, left top, left bottom, from(#f2dede), 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