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" >
< title > PCA biplot with < code > ggplot2< / code > — ggplot_pca • 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" / >
<!-- 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 -->
2020-04-13 21:09:56 +02:00
< 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
2020-04-13 21:09:56 +02:00
< 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 >
<!-- 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 >
< meta property = "og:title" content = "PCA biplot with <code>ggplot2</code> — 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." / >
2020-07-08 14:48:06 +02:00
< meta property = "og:image" content = "https://msberends.github.io/AMR/logo.svg" / >
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]-->
< / head >
2020-04-13 21:09:56 +02:00
< body data-spy = "scroll" data-target = "#toc" >
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 >
2020-07-30 12:37:01 +02:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.3.0< / 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" >
< span class = "fa fa-home" > < / span >
Home
< / a >
< / li >
< li class = "dropdown" >
< a href = "#" class = "dropdown-toggle" data-toggle = "dropdown" role = "button" aria-expanded = "false" >
< span class = "fa fa-question-circle" > < / span >
How to
< span class = "caret" > < / span >
< / a >
< ul class = "dropdown-menu" role = "menu" >
< li >
< a href = "../articles/AMR.html" >
< span class = "fa fa-directions" > < / span >
Conduct AMR analysis
< / a >
< / li >
< li >
< a href = "../articles/resistance_predict.html" >
< span class = "fa fa-dice" > < / span >
Predict antimicrobial resistance
< / a >
< / li >
< li >
< a href = "../articles/PCA.html" >
2020-03-08 09:12:11 +01:00
< 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" >
< span class = "fa fa-skull-crossbones" > < / span >
Determine multi-drug resistance (MDR)
< / a >
< / li >
< li >
< a href = "../articles/WHONET.html" >
< span class = "fa fa-globe-americas" > < / span >
Work with WHONET data
< / a >
< / li >
< li >
< a href = "../articles/SPSS.html" >
< span class = "fa fa-file-upload" > < / span >
Import data from SPSS/SAS/Stata
< / a >
< / li >
< li >
< a href = "../articles/EUCAST.html" >
< span class = "fa fa-exchange-alt" > < / span >
Apply EUCAST rules
< / a >
< / li >
< li >
< a href = "../reference/mo_property.html" >
< span class = "fa fa-bug" > < / span >
Get properties of a microorganism
< / a >
< / li >
< li >
< a href = "../reference/ab_property.html" >
< span class = "fa fa-capsules" > < / span >
Get properties of an antibiotic
< / a >
< / li >
< li >
< a href = "../articles/benchmarks.html" >
< span class = "fa fa-shipping-fast" > < / span >
Other: benchmarks
< / a >
< / li >
< / ul >
< / li >
< li >
2020-07-28 18:39:57 +02:00
< a href = "../reference/index.html" >
2020-03-07 21:48:21 +01:00
< span class = "fa fa-book-open" > < / span >
Manual
< / a >
< / li >
< li >
< a href = "../authors.html" >
< span class = "fa fa-users" > < / span >
Authors
< / a >
< / li >
< li >
2020-07-28 18:39:57 +02:00
< a href = "../news/index.html" >
2020-03-07 21:48:21 +01:00
< span class = "far fa far fa-newspaper" > < / span >
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" >
< span class = "fab fa fab fa-github" > < / span >
2020-03-07 21:48:21 +01:00
Source Code
< / a >
< / li >
< li >
2020-07-28 18:39:57 +02:00
< a href = "../survey.html" >
< span class = "fa fa-clipboard-list" > < / span >
2020-03-07 21:48:21 +01:00
2020-07-28 18:39:57 +02:00
Survey
2020-03-07 21:48:21 +01:00
< / a >
< / li >
< / ul >
< / div > <!-- /.nav - collapse -->
< / div > <!-- /.container -->
< / div > <!-- /.navbar -->
< / header >
< div class = "row" >
< div class = "col-md-9 contents" >
< div class = "page-header" >
< 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 >
< pre class = "usage" > < span class = 'fu' > ggplot_pca< / span > (
< span class = 'no' > x< / span > ,
< span class = 'kw' > choices< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 1< / span > :< span class = 'fl' > 2< / span > ,
< span class = 'kw' > scale< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ,
2020-03-08 11:18:59 +01:00
< span class = 'kw' > pc.biplot< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ,
2020-03-07 21:48:21 +01:00
< span class = 'kw' > labels< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
< span class = 'kw' > labels_textsize< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 3< / span > ,
< span class = 'kw' > labels_text_placement< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 1.5< / span > ,
< span class = 'kw' > groups< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > ,
2020-03-08 11:18:59 +01:00
< span class = 'kw' > ellipse< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ,
2020-03-07 21:48:21 +01:00
< span class = 'kw' > ellipse_prob< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 0.68< / span > ,
< span class = 'kw' > ellipse_size< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 0.5< / span > ,
2020-03-08 11:18:59 +01:00
< span class = 'kw' > ellipse_alpha< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 0.5< / span > ,
2020-03-07 21:48:21 +01:00
< span class = 'kw' > points_size< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 2< / span > ,
< span class = 'kw' > points_alpha< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 0.25< / span > ,
< span class = 'kw' > arrows< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ,
< span class = 'kw' > arrows_colour< / span > < span class = 'kw' > =< / span > < span class = 'st' > "darkblue"< / span > ,
< span class = 'kw' > arrows_size< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 0.5< / span > ,
< span class = 'kw' > arrows_textsize< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 3< / span > ,
2020-07-28 18:39:57 +02:00
< span class = 'kw' > arrows_textangled< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ,
2020-03-07 21:48:21 +01:00
< span class = 'kw' > arrows_alpha< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 0.75< / span > ,
< span class = 'kw' > base_textsize< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 10< / span > ,
< span class = 'no' > ...< / span >
)< / pre >
< 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 >
< td > < p > a logical to indicate whether a normal data ellipse should be drawn for each group (set with < code > groups< / code > )< / p > < / td >
< / 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 >
< td > < p > a logical to indicate whether arrows should be drawn< / p > < / td >
< / 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 >
< td > < p > a logical whether the text at the end of the arrows should be angled< / p > < / td >
< / 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 >
< td > < p > Parameters passed on to functions< / p > < / td >
< / 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 >
< li > < p > Added total amount of explained variance as a caption in the plot< / p > < / li >
2020-03-08 11:18:59 +01:00
< li > < p > Cleaned all syntax based on the < code > lintr< / code > package 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 >
2020-07-28 18:39:57 +02:00
< p > The colours for labels and points can be changed by adding another scale layer for colour, like < code > < a href = 'https://ggplot2.tidyverse.org/reference/scale_viridis.html' > scale_colour_viridis_d()< / a > < / code > or < code > < a href = 'https://ggplot2.tidyverse.org/reference/scale_brewer.html' > scale_colour_brewer()< / a > < / code > .< / p >
2020-03-07 21:48:21 +01:00
< h2 class = "hasAnchor" id = "maturing-lifecycle" > < a class = "anchor" href = "#maturing-lifecycle" > < / a > Maturing lifecycle< / h2 >
< p > < img src = 'figures/lifecycle_maturing.svg' style = margin-bottom:5px / > < br / >
2020-07-08 14:48:06 +02:00
The < a href = 'lifecycle.html' > lifecycle< / a > of this function is < strong > maturing< / strong > . The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome < a href = 'https://github.com/msberends/AMR/issues' > to suggest changes at our repository< / a > or < a href = 'AMR.html' > write us an email (see section 'Contact Us')< / a > .< / p >
2020-03-07 21:48:21 +01:00
< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
< pre class = "examples" > < span class = 'co' > # `example_isolates` is a dataset available in the AMR package.< / span >
< span class = 'co' > # See ?example_isolates.< / span >
< span class = 'co' > # See ?pca for more info about Principal Component Analysis (PCA).< / span >
2020-07-31 10:50:08 +02:00
< span class = 'kw' > if< / span > (< span class = 'fl' > FALSE< / span > ) {
< span class = 'fu' > < a href = 'https://rdrr.io/r/base/library.html' > library< / a > < / span > (< span class = 'no' > dplyr< / span > )
2020-07-28 18:39:57 +02:00
< span class = 'no' > pca_model< / span > < span class = 'kw' > < -< / span > < span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/filter.html' > filter< / a > < / span > (< span class = 'fu' > < a href = 'mo_property.html' > mo_genus< / a > < / span > (< span class = 'no' > mo< / span > ) < span class = 'kw' > ==< / span > < span class = 'st' > "Staphylococcus"< / span > ) < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/group_by.html' > group_by< / a > < / span > (< span class = 'kw' > species< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'mo_property.html' > mo_shortname< / a > < / span > (< span class = 'no' > mo< / span > )) < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/summarise_all.html' > summarise_if< / a > < / span > (< span class = 'no' > is.rsi< / span > , < span class = 'no' > resistance< / span > ) < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'pca.html' > pca< / a > < / span > (< span class = 'no' > FLC< / span > , < span class = 'no' > AMC< / span > , < span class = 'no' > CXM< / span > , < span class = 'no' > GEN< / span > , < span class = 'no' > TOB< / span > , < span class = 'no' > TMP< / span > , < span class = 'no' > SXT< / span > , < span class = 'no' > CIP< / span > , < span class = 'no' > TEC< / span > , < span class = 'no' > TCY< / span > , < span class = 'no' > ERY< / span > )
< span class = 'co' > # old (base R)< / span >
< span class = 'fu' > < a href = 'https://rdrr.io/r/stats/biplot.html' > biplot< / a > < / span > (< span class = 'no' > pca_model< / span > )
< span class = 'co' > # new < / span >
< span class = 'fu' > ggplot_pca< / span > (< span class = 'no' > pca_model< / span > )
< span class = 'kw' > if< / span > (< span class = 'fu' > < a href = 'https://rdrr.io/r/base/library.html' > require< / a > < / span > (< span class = 'st' > "ggplot2"< / span > )) {
< span class = 'fu' > ggplot_pca< / span > (< span class = 'no' > pca_model< / span > ) +
< span class = 'fu' > < a href = 'https://ggplot2.tidyverse.org/reference/scale_viridis.html' > scale_colour_viridis_d< / a > < / span > () +
< span class = 'fu' > < a href = 'https://ggplot2.tidyverse.org/reference/labs.html' > labs< / a > < / span > (< span class = 'kw' > title< / span > < span class = 'kw' > =< / span > < span class = 'st' > "Title here"< / span > )
}
2020-05-16 13:05:47 +02:00
}< / pre >
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" >
< p > Developed by < a href = 'https://www.rug.nl/staff/m.s.berends/' > Matthijs S. Berends< / a > , < a href = 'https://www.rug.nl/staff/c.f.luz/' > Christian F. Luz< / a > , < a href = 'https://www.rug.nl/staff/a.w.friedrich/' > Alexander W. Friedrich< / a > , < a href = 'https://www.rug.nl/staff/b.sinha/' > Bhanu N. M. Sinha< / a > , < a href = 'https://www.rug.nl/staff/c.j.albers/' > Casper J. Albers< / a > , < a href = 'https://www.rug.nl/staff/c.glasner/' > Corinna Glasner< / a > .< / p >
< / div >
< div class = "pkgdown" >
2020-05-16 13:05:47 +02:00
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.5.1.< / p >
2020-03-07 21:48:21 +01:00
< / div >
< / footer >
< / div >
< / body >
< / html >
