2020-03-07 21:48:21 +01:00
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
< html lang = "en" >
< head >
< meta charset = "utf-8" >
< meta http-equiv = "X-UA-Compatible" content = "IE=edge" >
< meta name = "viewport" content = "width=device-width, initial-scale=1.0" >
2021-01-18 16:57:56 +01:00
< title > PCA Biplot with ggplot2 — ggplot_pca • AMR (for R)< / title >
2020-03-07 21:48:21 +01:00
<!-- 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" / >
<!-- jquery -->
2020-04-13 21:09:56 +02:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity = "sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin = "anonymous" > < / script >
2020-03-07 21:48:21 +01:00
<!-- Bootstrap -->
2020-12-27 00:07:00 +01:00
< link href = "https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel = "stylesheet" crossorigin = "anonymous" / >
2020-03-07 21:48:21 +01:00
2020-12-21 22:46:29 +01:00
2020-12-24 23:29:10 +01:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity = "sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin = "anonymous" > < / script >
2020-12-21 22:46:29 +01:00
2020-04-13 21:09:56 +02:00
<!-- bootstrap - toc -->
< link rel = "stylesheet" href = "../bootstrap-toc.css" >
< script src = "../bootstrap-toc.js" > < / script >
2020-03-07 21:48:21 +01:00
<!-- Font Awesome icons -->
2020-04-13 21:09:56 +02:00
< 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" / >
2020-03-07 21:48:21 +01:00
<!-- clipboard.js -->
2020-04-13 21:09:56 +02:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity = "sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin = "anonymous" > < / script >
2020-03-07 21:48:21 +01:00
<!-- headroom.js -->
2020-04-13 21:09:56 +02:00
< 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 >
2020-03-07 21:48:21 +01:00
<!-- pkgdown -->
< link href = "../pkgdown.css" rel = "stylesheet" >
< script src = "../pkgdown.js" > < / script >
< link href = "../extra.css" rel = "stylesheet" >
< script src = "../extra.js" > < / script >
2021-01-18 16:57:56 +01:00
< meta property = "og:title" content = "PCA Biplot with ggplot2 — ggplot_pca" / >
2020-04-13 21:09:56 +02:00
< meta property = "og:description" content = "Produces a ggplot2 variant of a so-called biplot for PCA (principal component analysis), but is more flexible and more appealing than the base R biplot() function." / >
2020-09-29 23:35:46 +02:00
< meta property = "og:image" content = "https://msberends.github.io/AMR/logo.png" / >
2021-08-16 21:54:34 +02:00
< meta name = "twitter:card" content = "summary_large_image" / >
< meta name = "twitter:creator" content = "@msberends" / >
< meta name = "twitter:site" content = "@univgroningen" / >
2020-03-07 21:48:21 +01:00
2021-07-23 21:42:11 +02:00
2020-03-07 21:48:21 +01:00
<!-- 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]-->
2021-07-23 21:42:11 +02:00
2020-03-07 21:48:21 +01:00
< / head >
2020-04-13 21:09:56 +02:00
< body data-spy = "scroll" data-target = "#toc" >
2021-07-23 21:42:11 +02:00
2020-03-07 21:48:21 +01:00
< div class = "container template-reference-topic" >
< header >
< div class = "navbar navbar-default navbar-fixed-top" role = "navigation" >
< div class = "container" >
< div class = "navbar-header" >
< button type = "button" class = "navbar-toggle collapsed" data-toggle = "collapse" data-target = "#navbar" aria-expanded = "false" >
< span class = "sr-only" > Toggle navigation< / span >
< span class = "icon-bar" > < / span >
< span class = "icon-bar" > < / span >
< span class = "icon-bar" > < / span >
< / button >
< span class = "navbar-brand" >
< a class = "navbar-link" href = "../index.html" > AMR (for R)< / a >
2021-08-29 23:50:45 +02:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.7.1.9030< / span >
2020-03-07 21:48:21 +01:00
< / span >
< / div >
< div id = "navbar" class = "navbar-collapse collapse" >
< ul class = "nav navbar-nav" >
< li >
< a href = "../index.html" >
2021-07-23 21:42:11 +02:00
< span class = "fa fa-home" > < / span >
2020-03-07 21:48:21 +01:00
Home
< / a >
< / li >
< li class = "dropdown" >
< a href = "#" class = "dropdown-toggle" data-toggle = "dropdown" role = "button" aria-expanded = "false" >
2021-07-23 21:42:11 +02:00
< span class = "fa fa-question-circle" > < / span >
2020-03-07 21:48:21 +01:00
How to
< span class = "caret" > < / span >
< / a >
< ul class = "dropdown-menu" role = "menu" >
< li >
< a href = "../articles/AMR.html" >
2021-07-23 21:42:11 +02:00
< span class = "fa fa-directions" > < / span >
2020-03-07 21:48:21 +01:00
Conduct AMR analysis
< / a >
< / li >
< li >
< a href = "../articles/resistance_predict.html" >
2021-07-23 21:42:11 +02:00
< span class = "fa fa-dice" > < / span >
2020-03-07 21:48:21 +01:00
Predict antimicrobial resistance
< / a >
< / li >
2020-08-21 11:40:13 +02:00
< li >
< a href = "../articles/datasets.html" >
2021-07-23 21:42:11 +02:00
< span class = "fa fa-database" > < / span >
2020-08-21 11:40:13 +02:00
2020-09-03 20:59:21 +02:00
Data sets for download / own use
2020-08-21 11:40:13 +02:00
< / a >
< / li >
2020-03-07 21:48:21 +01:00
< li >
< a href = "../articles/PCA.html" >
2021-07-23 21:42:11 +02:00
< span class = "fa fa-compress" > < / span >
2020-03-07 21:48:21 +01:00
2020-03-08 09:12:11 +01:00
Conduct principal component analysis for AMR
2020-03-07 21:48:21 +01:00
< / a >
< / li >
< li >
< a href = "../articles/MDR.html" >
2021-07-23 21:42:11 +02:00
< span class = "fa fa-skull-crossbones" > < / span >
2020-03-07 21:48:21 +01:00
Determine multi-drug resistance (MDR)
< / a >
< / li >
< li >
< a href = "../articles/WHONET.html" >
2021-07-23 21:42:11 +02:00
< span class = "fa fa-globe-americas" > < / span >
2020-03-07 21:48:21 +01:00
Work with WHONET data
< / a >
< / li >
< li >
< a href = "../articles/SPSS.html" >
2021-07-23 21:42:11 +02:00
< span class = "fa fa-file-upload" > < / span >
2020-03-07 21:48:21 +01:00
Import data from SPSS/SAS/Stata
< / a >
< / li >
< li >
< a href = "../articles/EUCAST.html" >
2021-07-23 21:42:11 +02:00
< span class = "fa fa-exchange-alt" > < / span >
2020-03-07 21:48:21 +01:00
Apply EUCAST rules
< / a >
< / li >
< li >
< a href = "../reference/mo_property.html" >
2021-07-23 21:42:11 +02:00
< span class = "fa fa-bug" > < / span >
2020-03-07 21:48:21 +01:00
Get properties of a microorganism
< / a >
< / li >
< li >
< a href = "../reference/ab_property.html" >
2021-07-23 21:42:11 +02:00
< span class = "fa fa-capsules" > < / span >
2020-03-07 21:48:21 +01:00
Get properties of an antibiotic
< / a >
< / li >
< li >
< a href = "../articles/benchmarks.html" >
2021-07-23 21:42:11 +02:00
< span class = "fa fa-shipping-fast" > < / span >
2020-03-07 21:48:21 +01:00
Other: benchmarks
< / a >
< / li >
< / ul >
< / li >
< li >
2020-07-28 18:39:57 +02:00
< a href = "../reference/index.html" >
2021-07-23 21:42:11 +02:00
< span class = "fa fa-book-open" > < / span >
2020-03-07 21:48:21 +01:00
Manual
< / a >
< / li >
< li >
< a href = "../authors.html" >
2021-07-23 21:42:11 +02:00
< span class = "fa fa-users" > < / span >
2020-03-07 21:48:21 +01:00
Authors
< / a >
< / li >
< li >
2020-07-28 18:39:57 +02:00
< a href = "../news/index.html" >
2021-04-29 17:16:30 +02:00
< span class = "far fa-newspaper" > < / span >
2020-03-07 21:48:21 +01:00
Changelog
< / a >
< / li >
< / ul >
< ul class = "nav navbar-nav navbar-right" >
< li >
2020-07-08 14:48:06 +02:00
< a href = "https://github.com/msberends/AMR" >
2021-04-29 17:16:30 +02:00
< span class = "fab fa-github" > < / span >
2020-03-07 21:48:21 +01:00
Source Code
< / a >
< / li >
< / ul >
< / div > <!-- /.nav - collapse -->
< / div > <!-- /.container -->
< / div > <!-- /.navbar -->
< / header >
< div class = "row" >
< div class = "col-md-9 contents" >
< div class = "page-header" >
2021-01-18 16:57:56 +01:00
< h1 > PCA Biplot with < code > ggplot2< / code > < / h1 >
2020-07-08 14:48:06 +02:00
< small class = "dont-index" > Source: < a href = 'https://github.com/msberends/AMR/blob/master/R/ggplot_pca.R' > < code > R/ggplot_pca.R< / code > < / a > < / small >
2020-03-07 21:48:21 +01:00
< div class = "hidden name" > < code > ggplot_pca.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
2020-04-13 21:09:56 +02:00
< p > Produces a < code > ggplot2< / code > variant of a so-called < a href = 'https://en.wikipedia.org/wiki/Biplot' > biplot< / a > for PCA (principal component analysis), but is more flexible and more appealing than the base < span style = "R" > R< / span > < code > < a href = 'https://rdrr.io/r/stats/biplot.html' > biplot()< / a > < / code > function.< / p >
2020-03-07 21:48:21 +01:00
< / div >
2021-07-23 21:42:11 +02:00
< div class = "ref-usage sourceCode" > < pre class = 'sourceCode r' > < code > < span class = 'fu' > ggplot_pca< / span > < span class = 'op' > (< / span >
2020-10-19 17:09:19 +02:00
< span class = 'va' > x< / span > ,
choices < span class = 'op' > =< / span > < span class = 'fl' > 1< / span > < span class = 'op' > :< / span > < span class = 'fl' > 2< / span > ,
scale < span class = 'op' > =< / span > < span class = 'fl' > 1< / span > ,
pc.biplot < span class = 'op' > =< / span > < span class = 'cn' > TRUE< / span > ,
labels < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
labels_textsize < span class = 'op' > =< / span > < span class = 'fl' > 3< / span > ,
labels_text_placement < span class = 'op' > =< / span > < span class = 'fl' > 1.5< / span > ,
groups < span class = 'op' > =< / span > < span class = 'cn' > NULL< / span > ,
ellipse < span class = 'op' > =< / span > < span class = 'cn' > TRUE< / span > ,
ellipse_prob < span class = 'op' > =< / span > < span class = 'fl' > 0.68< / span > ,
ellipse_size < span class = 'op' > =< / span > < span class = 'fl' > 0.5< / span > ,
ellipse_alpha < span class = 'op' > =< / span > < span class = 'fl' > 0.5< / span > ,
points_size < span class = 'op' > =< / span > < span class = 'fl' > 2< / span > ,
points_alpha < span class = 'op' > =< / span > < span class = 'fl' > 0.25< / span > ,
arrows < span class = 'op' > =< / span > < span class = 'cn' > TRUE< / span > ,
arrows_colour < span class = 'op' > =< / span > < span class = 'st' > "darkblue"< / span > ,
arrows_size < span class = 'op' > =< / span > < span class = 'fl' > 0.5< / span > ,
arrows_textsize < span class = 'op' > =< / span > < span class = 'fl' > 3< / span > ,
arrows_textangled < span class = 'op' > =< / span > < span class = 'cn' > TRUE< / span > ,
arrows_alpha < span class = 'op' > =< / span > < span class = 'fl' > 0.75< / span > ,
base_textsize < span class = 'op' > =< / span > < span class = 'fl' > 10< / span > ,
< span class = 'va' > ...< / span >
2021-07-23 21:42:11 +02:00
< span class = 'op' > )< / span > < / code > < / pre > < / div >
2020-03-07 21:48:21 +01:00
< h2 class = "hasAnchor" id = "arguments" > < a class = "anchor" href = "#arguments" > < / a > Arguments< / h2 >
< table class = "ref-arguments" >
< colgroup > < col class = "name" / > < col class = "desc" / > < / colgroup >
< tr >
< th > x< / th >
< td > < p > an object returned by < code > < a href = 'pca.html' > pca()< / a > < / code > , < code > < a href = 'https://rdrr.io/r/stats/prcomp.html' > prcomp()< / a > < / code > or < code > < a href = 'https://rdrr.io/r/stats/princomp.html' > princomp()< / a > < / code > < / p > < / td >
< / tr >
< tr >
< th > choices< / th >
< td > < p > length 2 vector specifying the components to plot. Only the default
is a biplot in the strict sense.< / p > < / td >
< / tr >
< tr >
< th > scale< / th >
< td > < p > The variables are scaled by < code > lambda ^ scale< / code > and the
observations are scaled by < code > lambda ^ (1-scale)< / code > where
< code > lambda< / code > are the singular values as computed by
< code > < a href = 'https://rdrr.io/r/stats/princomp.html' > princomp< / a > < / code > . Normally < code > 0 < = scale < = 1< / code > , and a warning
will be issued if the specified < code > scale< / code > is outside this range.< / p > < / td >
< / tr >
2020-03-08 11:18:59 +01:00
< tr >
< th > pc.biplot< / th >
< td > < p > If true, use what Gabriel (1971) refers to as a "principal component
biplot", with < code > lambda = 1< / code > and observations scaled up by sqrt(n) and
variables scaled down by sqrt(n). Then inner products between
variables approximate covariances and distances between observations
approximate Mahalanobis distance.< / p > < / td >
< / tr >
2020-03-07 21:48:21 +01:00
< tr >
< th > labels< / th >
< td > < p > an optional vector of labels for the observations. If set, the labels will be placed below their respective points. When using the < code > < a href = 'pca.html' > pca()< / a > < / code > function as input for < code > x< / code > , this will be determined automatically based on the attribute < code > non_numeric_cols< / code > , see < code > < a href = 'pca.html' > pca()< / a > < / code > .< / p > < / td >
< / tr >
< tr >
< th > labels_textsize< / th >
< td > < p > the size of the text used for the labels< / p > < / td >
< / tr >
< tr >
< th > labels_text_placement< / th >
< td > < p > adjustment factor the placement of the variable names (< code > > =1< / code > means further away from the arrow head)< / p > < / td >
< / tr >
< tr >
< th > groups< / th >
< td > < p > an optional vector of groups for the labels, with the same length as < code > labels< / code > . If set, the points and labels will be coloured according to these groups. When using the < code > < a href = 'pca.html' > pca()< / a > < / code > function as input for < code > x< / code > , this will be determined automatically based on the attribute < code > non_numeric_cols< / code > , see < code > < a href = 'pca.html' > pca()< / a > < / code > .< / p > < / td >
< / tr >
< tr >
< th > ellipse< / th >
2021-05-12 18:15:03 +02:00
< td > < p > a < a href = 'https://rdrr.io/r/base/logical.html' > logical< / a > to indicate whether a normal data ellipse should be drawn for each group (set with < code > groups< / code > )< / p > < / td >
2020-03-07 21:48:21 +01:00
< / tr >
< tr >
< th > ellipse_prob< / th >
< td > < p > statistical size of the ellipse in normal probability< / p > < / td >
< / tr >
< tr >
< th > ellipse_size< / th >
< td > < p > the size of the ellipse line< / p > < / td >
< / tr >
< tr >
< th > ellipse_alpha< / th >
< td > < p > the alpha (transparency) of the ellipse line< / p > < / td >
< / tr >
2020-03-08 09:12:11 +01:00
< tr >
< th > points_size< / th >
< td > < p > the size of the points< / p > < / td >
< / tr >
2020-03-07 21:48:21 +01:00
< tr >
< th > points_alpha< / th >
< td > < p > the alpha (transparency) of the points< / p > < / td >
< / tr >
< tr >
< th > arrows< / th >
2021-05-12 18:15:03 +02:00
< td > < p > a < a href = 'https://rdrr.io/r/base/logical.html' > logical< / a > to indicate whether arrows should be drawn< / p > < / td >
2020-03-07 21:48:21 +01:00
< / tr >
< tr >
< th > arrows_colour< / th >
< td > < p > the colour of the arrow and their text< / p > < / td >
< / tr >
< tr >
< th > arrows_size< / th >
< td > < p > the size (thickness) of the arrow lines< / p > < / td >
< / tr >
< tr >
< th > arrows_textsize< / th >
< td > < p > the size of the text at the end of the arrows< / p > < / td >
< / tr >
2020-07-28 18:39:57 +02:00
< tr >
< th > arrows_textangled< / th >
2021-05-12 18:15:03 +02:00
< td > < p > a < a href = 'https://rdrr.io/r/base/logical.html' > logical< / a > whether the text at the end of the arrows should be angled< / p > < / td >
2020-07-28 18:39:57 +02:00
< / tr >
2020-03-07 21:48:21 +01:00
< tr >
< th > arrows_alpha< / th >
< td > < p > the alpha (transparency) of the arrows and their text< / p > < / td >
< / tr >
< tr >
< th > base_textsize< / th >
< td > < p > the text size for all plot elements except the labels and arrows< / p > < / td >
< / tr >
< tr >
< th > ...< / th >
2021-04-29 17:16:30 +02:00
< td > < p > arguments passed on to functions< / p > < / td >
2020-03-07 21:48:21 +01:00
< / tr >
< / table >
< h2 class = "hasAnchor" id = "source" > < a class = "anchor" href = "#source" > < / a > Source< / h2 >
< p > The < code > ggplot_pca()< / code > function is based on the < code > ggbiplot()< / code > function from the < code > ggbiplot< / code > package by Vince Vu, as found on GitHub: < a href = 'https://github.com/vqv/ggbiplot' > https://github.com/vqv/ggbiplot< / a > (retrieved: 2 March 2020, their latest commit: < a href = 'https://github.com/vqv/ggbiplot/commit/7325e880485bea4c07465a0304c470608fffb5d9' > < code > 7325e88< / code > < / a > ; 12 February 2015).< / p >
< p > As per their GPL-2 licence that demands documentation of code changes, the changes made based on the source code were:< / p > < ol >
< li > < p > Rewritten code to remove the dependency on packages < code > plyr< / code > , < code > scales< / code > and < code > grid< / code > < / p > < / li >
< li > < p > Parametrised more options, like arrow and ellipse settings< / p > < / li >
2020-12-22 00:51:17 +01:00
< li > < p > Hardened all input possibilities by defining the exact type of user input for every argument< / p > < / li >
2020-03-07 21:48:21 +01:00
< li > < p > Added total amount of explained variance as a caption in the plot< / p > < / li >
2020-10-19 17:09:19 +02:00
< li > < p > Cleaned all syntax based on the < code > lintr< / code > package, fixed grammatical errors and added integrity checks< / p > < / li >
2020-03-07 21:48:21 +01:00
< li > < p > Updated documentation< / p > < / li >
< / ol >
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
2021-03-15 07:23:21 +01:00
< p > The colours for labels and points can be changed by adding another scale layer for colour, such as < code > < a href = 'https://ggplot2.tidyverse.org/reference/scale_viridis.html' > scale_colour_viridis_d()< / a > < / code > and < code > < a href = 'https://ggplot2.tidyverse.org/reference/scale_brewer.html' > scale_colour_brewer()< / a > < / code > .< / p >
2021-03-07 13:52:39 +01:00
< h2 class = "hasAnchor" id = "stable-lifecycle" > < a class = "anchor" href = "#stable-lifecycle" > < / a > Stable Lifecycle< / h2 >
2020-03-07 21:48:21 +01:00
2021-03-07 13:52:39 +01:00
< p > < img src = 'figures/lifecycle_stable.svg' style = margin-bottom:5px / > < br / >
The < a href = 'lifecycle.html' > lifecycle< / a > of this function is < strong > stable< / strong > . In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.< / p >
< p > If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.< / p >
2020-03-07 21:48:21 +01:00
< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
2021-07-23 21:42:11 +02:00
< div class = "ref-examples sourceCode" > < pre class = 'sourceCode r' > < code > < span class = 'co' > # `example_isolates` is a data set available in the AMR package.< / span >
2020-03-07 21:48:21 +01:00
< span class = 'co' > # See ?example_isolates.< / span >
< span class = 'co' > # See ?pca for more info about Principal Component Analysis (PCA).< / span >
2021-05-24 09:00:11 +02:00
< span class = 'co' > # \donttest{< / span >
2020-10-19 17:09:19 +02:00
< span class = 'kw' > if< / span > < span class = 'op' > (< / span > < span class = 'kw' > < a href = 'https://rdrr.io/r/base/library.html' > require< / a > < / span > < span class = 'op' > (< / span > < span class = 'st' > < a href = 'https://dplyr.tidyverse.org' > "dplyr"< / a > < / span > < span class = 'op' > )< / span > < span class = 'op' > )< / span > < span class = 'op' > {< / span >
< span class = 'va' > pca_model< / span > < span class = 'op' > < -< / span > < span class = 'va' > example_isolates< / span > < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/filter.html' > filter< / a > < / span > < span class = 'op' > (< / span > < span class = 'fu' > < a href = 'mo_property.html' > mo_genus< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > mo< / span > < span class = 'op' > )< / span > < span class = 'op' > ==< / span > < span class = 'st' > "Staphylococcus"< / span > < span class = 'op' > )< / span > < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/group_by.html' > group_by< / a > < / span > < span class = 'op' > (< / span > species < span class = 'op' > =< / span > < span class = 'fu' > < a href = 'mo_property.html' > mo_shortname< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > mo< / span > < span class = 'op' > )< / span > < span class = 'op' > )< / span > < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/summarise_all.html' > summarise_if< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > is.rsi< / span > , < span class = 'va' > resistance< / span > < span class = 'op' > )< / span > < span class = 'op' > %> %< / span >
< span class = 'fu' > < a href = 'pca.html' > pca< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > FLC< / span > , < span class = 'va' > AMC< / span > , < span class = 'va' > CXM< / span > , < span class = 'va' > GEN< / span > , < span class = 'va' > TOB< / span > , < span class = 'va' > TMP< / span > , < span class = 'va' > SXT< / span > , < span class = 'va' > CIP< / span > , < span class = 'va' > TEC< / span > , < span class = 'va' > TCY< / span > , < span class = 'va' > ERY< / span > < span class = 'op' > )< / span >
2020-08-10 12:46:03 +02:00
2020-07-28 18:39:57 +02:00
< span class = 'co' > # old (base R)< / span >
2020-10-19 17:09:19 +02:00
< span class = 'fu' > < a href = 'https://rdrr.io/r/stats/biplot.html' > biplot< / a > < / span > < span class = 'op' > (< / span > < span class = 'va' > pca_model< / span > < span class = 'op' > )< / span >
2020-08-10 12:46:03 +02:00
2020-07-28 18:39:57 +02:00
< span class = 'co' > # new < / span >
2020-10-19 17:09:19 +02:00
< span class = 'fu' > ggplot_pca< / span > < span class = 'op' > (< / span > < span class = 'va' > pca_model< / span > < span class = 'op' > )< / span >
2020-08-10 12:46:03 +02:00
2021-04-29 17:16:30 +02:00
< span class = 'kw' > if< / span > < span class = 'op' > (< / span > < span class = 'kw' > < a href = 'https://rdrr.io/r/base/library.html' > require< / a > < / span > < span class = 'op' > (< / span > < span class = 'st' > < a href = 'https://ggplot2.tidyverse.org' > "ggplot2"< / a > < / span > < span class = 'op' > )< / span > < span class = 'op' > )< / span > < span class = 'op' > {< / span >
2020-10-19 17:09:19 +02:00
< span class = 'fu' > ggplot_pca< / span > < span class = 'op' > (< / span > < span class = 'va' > pca_model< / span > < span class = 'op' > )< / span > < span class = 'op' > +< / span >
< span class = 'fu' > < a href = 'https://ggplot2.tidyverse.org/reference/scale_viridis.html' > scale_colour_viridis_d< / a > < / span > < span class = 'op' > (< / span > < span class = 'op' > )< / span > < span class = 'op' > +< / span >
< span class = 'fu' > < a href = 'https://ggplot2.tidyverse.org/reference/labs.html' > labs< / a > < / span > < span class = 'op' > (< / span > title < span class = 'op' > =< / span > < span class = 'st' > "Title here"< / span > < span class = 'op' > )< / span >
< span class = 'op' > }< / span >
< span class = 'op' > }< / span >
2021-05-24 09:00:11 +02:00
< span class = 'co' > # }< / span >
2021-07-23 21:42:11 +02:00
< / code > < / pre > < / div >
2020-03-07 21:48:21 +01:00
< / div >
2020-04-13 21:09:56 +02:00
< div class = "col-md-3 hidden-xs hidden-sm" id = "pkgdown-sidebar" >
< nav id = "toc" data-toggle = "toc" class = "sticky-top" >
< h2 data-toc-skip > Contents< / h2 >
< / nav >
2020-03-07 21:48:21 +01:00
< / div >
< / div >
< footer >
< div class = "copyright" >
2021-07-23 21:42:11 +02:00
< p > < p > Developed by < a href = "https://www.rug.nl/staff/m.s.berends/" class = "external-link" > Matthijs S. Berends< / a > , < a href = "https://www.rug.nl/staff/c.f.luz/" class = "external-link" > Christian F. Luz< / a > , < a href = "https://www.rug.nl/staff/a.w.friedrich/" class = "external-link" > Alexander W. Friedrich< / a > , < a href = "https://www.rug.nl/staff/b.sinha/" class = "external-link" > Bhanu N. M. Sinha< / a > , < a href = "https://www.rug.nl/staff/c.j.albers/" class = "external-link" > Casper J. Albers< / a > , < a href = "https://www.rug.nl/staff/c.glasner/" class = "external-link" > Corinna Glasner< / a > .< / p > < / p >
2020-03-07 21:48:21 +01:00
< / div >
< div class = "pkgdown" >
2021-07-23 21:42:11 +02:00
< p > < p > Site built with < a href = "https://pkgdown.r-lib.org/" class = "external-link" > pkgdown< / a > 1.6.1.9001.< / p > < / p >
2020-03-07 21:48:21 +01:00
< / div >
< / footer >
< / div >
2021-07-23 21:42:11 +02:00
2020-03-07 21:48:21 +01:00
< / body >
< / html >
