2022-08-21 16:59:35 +02:00
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --> < html lang = "en" >
< head >
< meta http-equiv = "Content-Type" content = "text/html; charset=UTF-8" >
< meta charset = "utf-8" >
< meta http-equiv = "X-UA-Compatible" content = "IE=edge" >
< meta name = "viewport" content = "width=device-width, initial-scale=1, shrink-to-fit=no" >
< meta name = "description" content = "AMR" >
< title > How to conduct principal component analysis (PCA) for AMR • AMR (for R)< / title >
<!-- favicons --> < link rel = "icon" type = "image/png" sizes = "16x16" href = "../favicon-16x16.png" >
< link rel = "icon" type = "image/png" sizes = "32x32" href = "../favicon-32x32.png" >
< link rel = "apple-touch-icon" type = "image/png" sizes = "180x180" href = "../apple-touch-icon.png" >
< link rel = "apple-touch-icon" type = "image/png" sizes = "120x120" href = "../apple-touch-icon-120x120.png" >
< link rel = "apple-touch-icon" type = "image/png" sizes = "76x76" href = "../apple-touch-icon-76x76.png" >
< link rel = "apple-touch-icon" type = "image/png" sizes = "60x60" href = "../apple-touch-icon-60x60.png" >
< script src = "../deps/jquery-3.6.0/jquery-3.6.0.min.js" > < / script > < meta name = "viewport" content = "width=device-width, initial-scale=1, shrink-to-fit=no" >
2023-12-03 01:14:24 +01:00
< link href = "../deps/bootstrap-5.3.1/bootstrap.min.css" rel = "stylesheet" >
2024-02-13 13:53:34 +01:00
< script src = "../deps/bootstrap-5.3.1/bootstrap.bundle.min.js" > < / script > < link href = "../deps/Fira_Code-0.4.8/font.css" rel = "stylesheet" >
2022-08-21 16:59:35 +02:00
<!-- Font Awesome icons --> < link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity = "sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin = "anonymous" >
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity = "sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin = "anonymous" >
2022-12-16 16:17:49 +01:00
<!-- bootstrap - toc --> < script src = "https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity = "sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin = "anonymous" > < / script > <!-- headroom.js --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity = "sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin = "anonymous" > < / script > < script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity = "sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin = "anonymous" > < / script > <!-- clipboard.js --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity = "sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin = "anonymous" > < / script > <!-- search --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity = "sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin = "anonymous" > < / script > < script src = "https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity = "sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin = "anonymous" > < / script > < script src = "https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity = "sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin = "anonymous" > < / script > <!-- pkgdown --> < script src = "../pkgdown.js" > < / script > < link href = "../extra.css" rel = "stylesheet" >
2022-08-21 16:59:35 +02:00
< script src = "../extra.js" > < / script > < meta property = "og:title" content = "How to conduct principal component analysis (PCA) for AMR" >
< meta property = "og:description" content = "AMR" >
< meta property = "og:image" content = "https://msberends.github.io/AMR/logo.svg" >
< meta name = "twitter:card" content = "summary_large_image" >
< meta name = "twitter:creator" content = "@msberends" >
2022-10-05 12:32:07 +02:00
< meta name = "twitter:site" content = "@msberends" >
2022-08-21 16:59:35 +02:00
<!-- mathjax --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity = "sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin = "anonymous" > < / script > < script src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity = "sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin = "anonymous" > < / script > <!-- [if lt IE 9]>
< script src = "https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js" > < / script >
< script src = "https://oss.maxcdn.com/respond/1.4.2/respond.min.js" > < / script >
<![endif]-->
< / head >
< body >
< a href = "#main" class = "visually-hidden-focusable" > Skip to contents< / a >
< nav class = "navbar fixed-top navbar-dark navbar-expand-lg bg-primary" > < div class = "container" >
< a class = "navbar-brand me-2" href = "../index.html" > AMR (for R)< / a >
2024-02-24 19:32:41 +01:00
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 2.1.1.9009< / small >
2022-08-21 16:59:35 +02:00
< button class = "navbar-toggler" type = "button" data-bs-toggle = "collapse" data-bs-target = "#navbar" aria-controls = "navbar" aria-expanded = "false" aria-label = "Toggle navigation" >
< span class = "navbar-toggler-icon" > < / span >
< / button >
< div id = "navbar" class = "collapse navbar-collapse ms-3" >
< ul class = "navbar-nav me-auto" >
< li class = "active nav-item dropdown" >
< a href = "#" class = "nav-link dropdown-toggle" data-bs-toggle = "dropdown" role = "button" aria-expanded = "false" aria-haspopup = "true" id = "dropdown--how-to" >
< span class = "fa fa-question-circle" > < / span >
How to
< / a >
< div class = "dropdown-menu" aria-labelledby = "dropdown--how-to" >
< a class = "dropdown-item" href = "../articles/AMR.html" >
< span class = "fa fa-directions" > < / span >
2023-01-23 20:14:37 +01:00
Conduct AMR Analysis
2022-08-21 16:59:35 +02:00
< / a >
2023-02-08 17:01:47 +01:00
< a class = "dropdown-item" href = "../reference/antibiogram.html" >
< span class = "fa fa-file-prescription" > < / span >
Generate Antibiogram (Trad./Syndromic/WISCA)
< / a >
2022-08-21 16:59:35 +02:00
< a class = "dropdown-item" href = "../articles/resistance_predict.html" >
< span class = "fa fa-dice" > < / span >
2023-01-23 20:14:37 +01:00
Predict Antimicrobial Resistance
2022-08-21 16:59:35 +02:00
< / a >
< a class = "dropdown-item" href = "../articles/datasets.html" >
< span class = "fa fa-database" > < / span >
2023-02-26 21:34:01 +01:00
Download Data Sets for Own Use
< / a >
< a class = "dropdown-item" href = "../reference/AMR-options.html" >
< span class = "fa fa-gear" > < / span >
Set User- Or Team-specific Package Settings
2022-08-21 16:59:35 +02:00
< / a >
< a class = "dropdown-item" href = "../articles/PCA.html" >
< span class = "fa fa-compress" > < / span >
2023-01-23 20:14:37 +01:00
Conduct Principal Component Analysis for AMR
2022-08-21 16:59:35 +02:00
< / a >
< a class = "dropdown-item" href = "../articles/MDR.html" >
< span class = "fa fa-skull-crossbones" > < / span >
2023-01-23 20:14:37 +01:00
Determine Multi-Drug Resistance (MDR)
2022-08-21 16:59:35 +02:00
< / a >
< a class = "dropdown-item" href = "../articles/WHONET.html" >
< span class = "fa fa-globe-americas" > < / span >
2023-01-23 20:14:37 +01:00
Work with WHONET Data
2022-08-21 16:59:35 +02:00
< / a >
< a class = "dropdown-item" href = "../articles/EUCAST.html" >
< span class = "fa fa-exchange-alt" > < / span >
2023-01-23 20:14:37 +01:00
Apply Eucast Rules
2022-08-21 16:59:35 +02:00
< / a >
< a class = "dropdown-item" href = "../reference/mo_property.html" >
< span class = "fa fa-bug" > < / span >
2023-01-23 20:14:37 +01:00
Get Taxonomy of a Microorganism
2022-08-21 16:59:35 +02:00
< / a >
< a class = "dropdown-item" href = "../reference/ab_property.html" >
< span class = "fa fa-capsules" > < / span >
2023-01-23 20:14:37 +01:00
Get Properties of an Antibiotic Drug
2022-08-21 16:59:35 +02:00
< / a >
2022-11-13 08:54:32 +01:00
< a class = "dropdown-item" href = "../reference/av_property.html" >
< span class = "fa fa-capsules" > < / span >
2023-01-23 20:14:37 +01:00
Get Properties of an Antiviral Drug
2022-11-13 08:54:32 +01:00
< / a >
2022-08-21 16:59:35 +02:00
< / div >
< / li >
2023-05-24 16:03:18 +02:00
< li class = "nav-item dropdown" >
< a href = "#" class = "nav-link dropdown-toggle" data-bs-toggle = "dropdown" role = "button" aria-expanded = "false" aria-haspopup = "true" id = "dropdown--with-other-pkgs" >
2023-05-27 10:53:23 +02:00
< span class = "fa fa-layer-group" > < / span >
2023-05-24 16:03:18 +02:00
With other pkgs
< / a >
< div class = "dropdown-menu" aria-labelledby = "dropdown--with-other-pkgs" >
< a class = "dropdown-item" href = "../articles/other_pkg.html" >
2023-05-27 10:53:23 +02:00
< span class = "fa fa-layer-group" > < / span >
2023-05-24 16:03:18 +02:00
AMR & dplyr/tidyverse
< / a >
< a class = "dropdown-item" href = "../articles/other_pkg.html" >
2023-05-27 10:53:23 +02:00
< span class = "fa fa-layer-group" > < / span >
2023-05-24 16:03:18 +02:00
AMR & data.table
< / a >
< a class = "dropdown-item" href = "../articles/other_pkg.html" >
2023-05-27 10:53:23 +02:00
< span class = "fa fa-layer-group" > < / span >
2023-05-24 16:03:18 +02:00
AMR & tidymodels
< / a >
< a class = "dropdown-item" href = "../articles/other_pkg.html" >
2023-05-27 10:53:23 +02:00
< span class = "fa fa-layer-group" > < / span >
2023-05-24 16:03:18 +02:00
AMR & base R
< / a >
< / div >
< / li >
2022-08-21 16:59:35 +02:00
< li class = "nav-item" >
< a class = "nav-link" href = "../reference/index.html" >
< span class = "fa fa-book-open" > < / span >
Manual
< / a >
< / li >
< li class = "nav-item" >
< a class = "nav-link" href = "../authors.html" >
< span class = "fa fa-users" > < / span >
Authors
< / a >
< / li >
2023-05-24 16:03:18 +02:00
< / ul >
< form class = "form-inline my-2 my-lg-0" role = "search" >
< input type = "search" class = "form-control me-sm-2" aria-label = "Toggle navigation" name = "search-input" data-search-index = "../search.json" id = "search-input" placeholder = "Search for" autocomplete = "off" >
< / form >
< ul class = "navbar-nav" >
2022-08-21 16:59:35 +02:00
< li class = "nav-item" >
< a class = "nav-link" href = "../news/index.html" >
< span class = "far fa far fa-newspaper" > < / span >
Changelog
< / a >
< / li >
< li class = "nav-item" >
< a class = "external-link nav-link" href = "https://github.com/msberends/AMR" >
< span class = "fab fa fab fa-github" > < / span >
Source Code
< / a >
< / li >
< / ul >
< / div >
< / div >
< / nav > < div class = "container template-article" >
< div class = "row" >
< main id = "main" class = "col-md-9" > < div class = "page-header" >
< img src = "../logo.svg" class = "logo" alt = "" > < h1 > How to conduct principal component analysis (PCA) for AMR< / h1 >
< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/vignettes/PCA.Rmd" class = "external-link" > < code > vignettes/PCA.Rmd< / code > < / a > < / small >
< div class = "d-none name" > < code > PCA.Rmd< / code > < / div >
< / div >
2022-10-29 14:24:08 +02:00
< p > < strong > NOTE: This page will be updated soon, as the pca() function
is currently being developed.< / strong > < / p >
2022-08-21 16:59:35 +02:00
< div class = "section level2" >
< h2 id = "introduction" > Introduction< a class = "anchor" aria-label = "anchor" href = "#introduction" > < / a >
< / h2 >
< / div >
< div class = "section level2" >
< h2 id = "transforming" > Transforming< a class = "anchor" aria-label = "anchor" href = "#transforming" > < / a >
< / h2 >
2022-10-29 14:24:08 +02:00
< p > For PCA, we need to transform our AMR data first. This is what the
< code > example_isolates< / code > data set in this package looks like:< / p >
2022-08-21 16:59:35 +02:00
< div class = "sourceCode" id = "cb1" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > library< / a > < / span > < span class = "op" > (< / span > < span class = "va" > < a href = "https://msberends.github.io/AMR/" > AMR< / a > < / span > < span class = "op" > )< / span > < / span >
< span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > library< / a > < / span > < span class = "op" > (< / span > < span class = "va" > < a href = "https://dplyr.tidyverse.org" class = "external-link" > dplyr< / a > < / span > < span class = "op" > )< / span > < / span >
< span > < span class = "fu" > < a href = "https://pillar.r-lib.org/reference/glimpse.html" class = "external-link" > glimpse< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > < span class = "op" > )< / span > < / span >
2023-02-18 13:17:35 +01:00
< span > < span class = "co" > #> Rows: 2,000< / span > < / span >
< span > < span class = "co" > #> Columns: 46< / span > < / span >
< span > < span class = "co" > #> $ date < span style = "color: #949494; font-style: italic;" > < date> < / span > 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-01-13, 2…< / span > < / span >
< span > < span class = "co" > #> $ patient < span style = "color: #949494; font-style: italic;" > < chr> < / span > "A77334", "A77334", "067927", "067927", "067927", "067927", "4…< / span > < / span >
< span > < span class = "co" > #> $ age < span style = "color: #949494; font-style: italic;" > < dbl> < / span > 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 71, 75, 50…< / span > < / span >
< span > < span class = "co" > #> $ gender < span style = "color: #949494; font-style: italic;" > < chr> < / span > "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M", "M", "M…< / span > < / span >
< span > < span class = "co" > #> $ ward < span style = "color: #949494; font-style: italic;" > < chr> < / span > "Clinical", "Clinical", "ICU", "ICU", "ICU", "ICU", "Clinical"…< / span > < / span >
< span > < span class = "co" > #> $ mo < span style = "color: #949494; font-style: italic;" > < mo> < / span > "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STPHY_EPDR",…< / span > < / span >
< span > < span class = "co" > #> $ PEN < span style = "color: #949494; font-style: italic;" > < sir> < / span > R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, S,…< / span > < / span >
< span > < span class = "co" > #> $ OXA < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…< / span > < / span >
< span > < span class = "co" > #> $ FLC < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, NA, R, R…< / span > < / span >
< span > < span class = "co" > #> $ AMX < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N…< / span > < / span >
< span > < span class = "co" > #> $ AMC < span style = "color: #949494; font-style: italic;" > < sir> < / span > I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, I, NA, N…< / span > < / span >
< span > < span class = "co" > #> $ AMP < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N…< / span > < / span >
< span > < span class = "co" > #> $ TZP < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…< / span > < / span >
< span > < span class = "co" > #> $ CZO < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,…< / span > < / span >
< span > < span class = "co" > #> $ FEP < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…< / span > < / span >
< span > < span class = "co" > #> $ CXM < span style = "color: #949494; font-style: italic;" > < sir> < / span > I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R, R, S, S…< / span > < / span >
< span > < span class = "co" > #> $ FOX < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,…< / span > < / span >
< span > < span class = "co" > #> $ CTX < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…< / span > < / span >
< span > < span class = "co" > #> $ CAZ < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S, R, R, …< / span > < / span >
< span > < span class = "co" > #> $ CRO < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…< / span > < / span >
< span > < span class = "co" > #> $ GEN < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…< / span > < / span >
< span > < span class = "co" > #> $ TOB < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA, NA, NA…< / span > < / span >
< span > < span class = "co" > #> $ AMK < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…< / span > < / span >
< span > < span class = "co" > #> $ KAN < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…< / span > < / span >
< span > < span class = "co" > #> $ TMP < span style = "color: #949494; font-style: italic;" > < sir> < / span > R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R, R, R, …< / span > < / span >
< span > < span class = "co" > #> $ SXT < span style = "color: #949494; font-style: italic;" > < sir> < / span > R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, S, NA, N…< / span > < / span >
< span > < span class = "co" > #> $ NIT < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R,…< / span > < / span >
< span > < span class = "co" > #> $ FOS < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…< / span > < / span >
< span > < span class = "co" > #> $ LNZ < span style = "color: #949494; font-style: italic;" > < sir> < / span > R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…< / span > < / span >
< span > < span class = "co" > #> $ CIP < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, NA, S, S…< / span > < / span >
< span > < span class = "co" > #> $ MFX < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…< / span > < / span >
< span > < span class = "co" > #> $ VAN < span style = "color: #949494; font-style: italic;" > < sir> < / span > R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S, S, S, …< / span > < / span >
< span > < span class = "co" > #> $ TEC < span style = "color: #949494; font-style: italic;" > < sir> < / span > R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…< / span > < / span >
< span > < span class = "co" > #> $ TCY < span style = "color: #949494; font-style: italic;" > < sir> < / span > R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S, I, R, …< / span > < / span >
< span > < span class = "co" > #> $ TGC < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA…< / span > < / span >
< span > < span class = "co" > #> $ DOX < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA…< / span > < / span >
< span > < span class = "co" > #> $ ERY < span style = "color: #949494; font-style: italic;" > < sir> < / span > R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,…< / span > < / span >
< span > < span class = "co" > #> $ CLI < span style = "color: #949494; font-style: italic;" > < sir> < / span > R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, R, R, NA…< / span > < / span >
< span > < span class = "co" > #> $ AZM < span style = "color: #949494; font-style: italic;" > < sir> < / span > R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,…< / span > < / span >
< span > < span class = "co" > #> $ IPM < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…< / span > < / span >
< span > < span class = "co" > #> $ MEM < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…< / span > < / span >
< span > < span class = "co" > #> $ MTR < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…< / span > < / span >
< span > < span class = "co" > #> $ CHL < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…< / span > < / span >
< span > < span class = "co" > #> $ COL < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R, R, R, …< / span > < / span >
< span > < span class = "co" > #> $ MUP < span style = "color: #949494; font-style: italic;" > < sir> < / span > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…< / span > < / span >
< span > < span class = "co" > #> $ RIF < span style = "color: #949494; font-style: italic;" > < sir> < / span > R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…< / span > < / span > < / code > < / pre > < / div >
2022-10-29 14:24:08 +02:00
< p > Now to transform this to a data set with only resistance percentages
per taxonomic order and genus:< / p >
2022-08-21 16:59:35 +02:00
< div class = "sourceCode" id = "cb2" > < pre class = "downlit sourceCode r" >
2022-08-28 22:45:38 +02:00
< code class = "sourceCode R" > < span > < span class = "va" > resistance_data< / span > < span class = "op" > < -< / span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/group_by.html" class = "external-link" > group_by< / a > < / span > < span class = "op" > (< / span > < / span >
< span > order < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_order< / a > < / span > < span class = "op" > (< / span > < span class = "va" > mo< / span > < span class = "op" > )< / span > , < span class = "co" > # group on anything, like order< / span > < / span >
< span > genus < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_genus< / a > < / span > < span class = "op" > (< / span > < span class = "va" > mo< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "co" > # and genus as we do here< / span > < / span >
2023-01-21 23:53:21 +01:00
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/summarise_all.html" class = "external-link" > summarise_if< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is.sir< / span > , < span class = "va" > resistance< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "co" > # then get resistance of all drugs< / span > < / span >
2022-08-28 22:45:38 +02:00
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < / span >
< span > < span class = "va" > order< / span > , < span class = "va" > genus< / span > , < span class = "va" > AMC< / span > , < span class = "va" > CXM< / span > , < span class = "va" > CTX< / span > ,< / span >
< span > < span class = "va" > CAZ< / span > , < span class = "va" > GEN< / span > , < span class = "va" > TOB< / span > , < span class = "va" > TMP< / span > , < span class = "va" > SXT< / span > < / span >
< span > < span class = "op" > )< / span > < span class = "co" > # and select only relevant columns< / span > < / span >
2022-08-21 16:59:35 +02:00
< span > < / span >
< span > < span class = "fu" > < a href = "https://rdrr.io/r/utils/head.html" class = "external-link" > head< / a > < / span > < span class = "op" > (< / span > < span class = "va" > resistance_data< / span > < span class = "op" > )< / span > < / span >
2023-02-18 13:17:35 +01:00
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 6 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # Groups: order [5]< / span > < / span > < / span >
< span > < span class = "co" > #> order genus AMC CXM CTX CAZ GEN TOB TMP SXT< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > (unknown order) (unknown ge… < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > Actinomycetales Schaalia < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > Bacteroidales Bacteroides < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > Campylobacterales Campylobact… < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > Caryophanales Gemella < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > Caryophanales Listeria < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < span style = "color: #BB0000;" > NA< / span > < / span > < / span > < / code > < / pre > < / div >
2022-08-21 16:59:35 +02:00
< / div >
< div class = "section level2" >
< h2 id = "perform-principal-component-analysis" > Perform principal component analysis< a class = "anchor" aria-label = "anchor" href = "#perform-principal-component-analysis" > < / a >
< / h2 >
2022-10-29 14:24:08 +02:00
< p > The new < code > < a href = "../reference/pca.html" > pca()< / a > < / code > function will automatically filter on rows
that contain numeric values in all selected variables, so we now only
need to do:< / p >
2022-08-21 16:59:35 +02:00
< div class = "sourceCode" id = "cb3" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "va" > pca_result< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "../reference/pca.html" > pca< / a > < / span > < span class = "op" > (< / span > < span class = "va" > resistance_data< / span > < span class = "op" > )< / span > < / span >
2023-02-22 14:47:35 +01:00
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> "TMP", and "TOB". Total observations available: 7.< / span > < / span > < / code > < / pre > < / div >
2022-10-29 14:24:08 +02:00
< p > The result can be reviewed with the good old < code > < a href = "https://rdrr.io/r/base/summary.html" class = "external-link" > summary()< / a > < / code >
function:< / p >
2022-08-21 16:59:35 +02:00
< div class = "sourceCode" id = "cb4" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/summary.html" class = "external-link" > summary< / a > < / span > < span class = "op" > (< / span > < span class = "va" > pca_result< / span > < span class = "op" > )< / span > < / span >
2023-02-18 13:17:35 +01:00
< span > < span class = "co" > #> Groups (n=4, named as 'order'):< / span > < / span >
< span > < span class = "co" > #> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"< / span > < / span >
< span > < span class = "co" > #> Importance of components:< / span > < / span >
< span > < span class = "co" > #> PC1 PC2 PC3 PC4 PC5 PC6 PC7< / span > < / span >
2023-12-03 01:14:24 +01:00
< span > < span class = "co" > #> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16< / span > < / span >
2023-02-18 13:17:35 +01:00
< span > < span class = "co" > #> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00< / span > < / span >
< span > < span class = "co" > #> Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00< / span > < / span > < / code > < / pre > < / div >
< pre > < code > < span > < span class = "co" > #> Groups (n=4, named as 'order'):< / span > < / span >
< span > < span class = "co" > #> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"< / span > < / span > < / code > < / pre >
2022-10-29 14:24:08 +02:00
< p > Good news. The first two components explain a total of 93.3% of the
variance (see the PC1 and PC2 values of the < em > Proportion of
Variance< / em > . We can create a so-called biplot with the base R
< code > < a href = "https://rdrr.io/r/stats/biplot.html" class = "external-link" > biplot()< / a > < / code > function, to see which antimicrobial resistance
per drug explain the difference per microorganism.< / p >
2022-08-21 16:59:35 +02:00
< / div >
< div class = "section level2" >
< h2 id = "plotting-the-results" > Plotting the results< a class = "anchor" aria-label = "anchor" href = "#plotting-the-results" > < / a >
< / h2 >
< div class = "sourceCode" id = "cb6" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/stats/biplot.html" class = "external-link" > biplot< / a > < / span > < span class = "op" > (< / span > < span class = "va" > pca_result< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< p > < img src = "PCA_files/figure-html/unnamed-chunk-5-1.png" width = "750" > < / p >
2022-10-29 14:24:08 +02:00
< p > But we can’
better with our new < code > < a href = "../reference/ggplot_pca.html" > ggplot_pca()< / a > < / code > function, that
automatically adds the right labels and even groups:< / p >
2022-08-21 16:59:35 +02:00
< div class = "sourceCode" id = "cb7" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "../reference/ggplot_pca.html" > ggplot_pca< / a > < / span > < span class = "op" > (< / span > < span class = "va" > pca_result< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< p > < img src = "PCA_files/figure-html/unnamed-chunk-6-1.png" width = "750" > < / p >
< p > You can also print an ellipse per group, and edit the appearance:< / p >
< div class = "sourceCode" id = "cb8" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "../reference/ggplot_pca.html" > ggplot_pca< / a > < / span > < span class = "op" > (< / span > < span class = "va" > pca_result< / span > , ellipse < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < span class = "op" > +< / span > < / span >
< span > < span class = "fu" > ggplot2< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://ggplot2.tidyverse.org/reference/labs.html" class = "external-link" > labs< / a > < / span > < span class = "op" > (< / span > title < span class = "op" > =< / span > < span class = "st" > "An AMR/PCA biplot!"< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< p > < img src = "PCA_files/figure-html/unnamed-chunk-7-1.png" width = "750" > < / p >
< / div >
< / main > < aside class = "col-md-3" > < nav id = "toc" > < h2 > On this page< / h2 >
< / nav > < / aside >
< / div >
< footer > < div class = "pkgdown-footer-left" >
< p > < / p >
2022-12-11 11:50:34 +01:00
< p > < code > AMR< / code > (for R). Free and open-source, licenced under the < a target = "_blank" href = "https://github.com/msberends/AMR/blob/main/LICENSE" class = "external-link" > GNU General Public License version 2.0 (GPL-2)< / a > .< br > Developed at the < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > University of Groningen< / a > and < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > University Medical Center Groningen< / a > in The Netherlands.< / p >
2022-08-21 16:59:35 +02:00
< / div >
< div class = "pkgdown-footer-right" >
< p > < / p >
2022-12-11 11:50:34 +01:00
< p > < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style = "max-width: 150px;" > < / a > < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style = "max-width: 150px;" > < / a > < / p >
2022-08-21 16:59:35 +02:00
< / div >
< / footer >
< / div >
< / body >
< / html >
