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cbPalettes.html
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<title>Ben Anderson</title>
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<h1 class="title toc-ignore">Ben Anderson</h1>
<h4 class="author"><em>Colour Blind Palettes for Plots (Contact: <a href="mailto:b.anderson@soton.ac.uk">b.anderson@soton.ac.uk</a>, <code>@dataknut</code>)</em></h4>
<h4 class="date"><em>Last run at: 2019-02-19 16:21:17</em></h4>
</div>
<div id="colour-blind-palettes" class="section level1">
<h1><span class="header-section-number">1</span> Colour Blind palettes</h1>
<p>Obviously these aid interpretation of plots by those who are colour blind but the <a href="http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/#a-colorblind-friendly-palette">palettes</a> are also useful clear defaults. Note that there are 8 colours in each palette:</p>
<ul>
<li>palette with grey: #999999, #E69F00, #56B4E9, #009E73, #F0E442, #0072B2, #D55E00, #CC79A7</li>
<li>palette with black: #000000, #E69F00, #56B4E9, #009E73, #F0E442, #0072B2, #D55E00, #CC79A7</li>
</ul>
<p>Source: <a href="http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/#a-colorblind-friendly-palette" class="uri">http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/#a-colorblind-friendly-palette</a></p>
<p>This means that a plot with more than this number of factors will run out of colours (see below).</p>
<div id="grey-palette" class="section level2">
<h2><span class="header-section-number">1.1</span> Grey palette</h2>
<p>This is a cross-reference to Figure <a href="#fig:plot1">1.1</a> which uses the grey palette.</p>
<pre class="r"><code>df <- mtcars
df$auto <- ifelse(df$am == 0, "Automatic", "Manual") # set labels
p <- ggplot2::ggplot(df, aes(x = mpg, y = disp, colour = as.factor(carb))) +
guides(colour = guide_legend(title = "Number of carburetors:")) +
theme(legend.position="bottom") +
scale_colour_manual(values=cbgPalette) + # use colour-blind friendly grey palette
geom_point() # <- make the plot in an object first
p + labs(x = "Miles/(US) gallon", y = "Displacement (cu.in.)") + facet_grid(auto ~ .) # <- draw the plot and add more features</code></pre>
<div class="figure"><span id="fig:plot1"></span>
<img src="cbPalettes_files/figure-html/plot1-1.png" alt="Scatter plot of mpg by displacement (grey palette)" width="672" />
<p class="caption">
Figure 1.1: Scatter plot of mpg by displacement (grey palette)
</p>
</div>
</div>
<div id="black-palette" class="section level2">
<h2><span class="header-section-number">1.2</span> Black palette</h2>
<p>This is a cross-reference to Figure <a href="#fig:plot2">1.2</a> which uses the black palette.</p>
<pre class="r"><code>p <- ggplot2::ggplot(df, aes(x = mpg, y = disp, colour = as.factor(carb))) +
guides(colour = guide_legend(title = "Number of carburetors:")) +
theme(legend.position="bottom") +
scale_colour_manual(values=cbbPalette) + # use colour-blind friendly grey palette
geom_point() # <- make the plot in an object first
p + labs(x = "Miles/(US) gallon", y = "Displacement (cu.in.)") + facet_grid(auto ~ .) # <- draw the plot and add more features</code></pre>
<div class="figure"><span id="fig:plot2"></span>
<img src="cbPalettes_files/figure-html/plot2-1.png" alt="Scatter plot of mpg by displacement (black palette)" width="672" />
<p class="caption">
Figure 1.2: Scatter plot of mpg by displacement (black palette)
</p>
</div>
</div>
</div>
<div id="using-viridis" class="section level1">
<h1><span class="header-section-number">2</span> Using viridis</h1>
<p>An alternative to the palettes is the <a href="https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html">viridis</a> package <span class="citation">(Garnier 2018)</span>. This has the benefit of not having a small number of colours although Figure <a href="#fig:plot3">2.1</a> doesn’t really demonstrate this!</p>
<pre class="r"><code>library(viridis)</code></pre>
<pre><code>## Loading required package: viridisLite</code></pre>
<pre class="r"><code>p <- ggplot2::ggplot(df, aes(x = mpg, y = disp, colour = carb)) +
guides(colour = guide_legend(title = "Number of carburetors:")) +
theme(legend.position="bottom") +
scale_colour_viridis() + # use viridis
geom_point() # <- make the plot in an object first
p + labs(x = "Miles/(US) gallon", y = "Displacement (cu.in.)") + facet_grid(auto ~ .) # <- draw the plot and add more features</code></pre>
<div class="figure"><span id="fig:plot3"></span>
<img src="cbPalettes_files/figure-html/plot3-1.png" alt="Scatter plot of mpg by displacement (viridis palette)" width="672" />
<p class="caption">
Figure 2.1: Scatter plot of mpg by displacement (viridis palette)
</p>
</div>
</div>
<div id="summary" class="section level1">
<h1><span class="header-section-number">3</span> Summary</h1>
<p>Personally I prefer the <a href="http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/#a-colorblind-friendly-palette">colour blind palettes</a> if I have a small number of categories (less than 8) but usually use <a href="https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html">viridis</a> if I have more than that and if I have continuous data.</p>
</div>
<div id="ackowledgement" class="section level1">
<h1><span class="header-section-number">4</span> Ackowledgement</h1>
<p>Uses ggplot2 <span class="citation">(Wickham 2009)</span> and associated mtcars dataset to draw plots. Palettes available from <a href="http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/#a-colorblind-friendly-palette" class="uri">http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/#a-colorblind-friendly-palette</a></p>
</div>
<div id="references" class="section level1 unnumbered">
<h1>References</h1>
<div id="refs" class="references">
<div id="ref-viridis">
<p>Garnier, Simon. 2018. <em>Viridis: Default Color Maps from ’Matplotlib’</em>. <a href="https://CRAN.R-project.org/package=viridis" class="uri">https://CRAN.R-project.org/package=viridis</a>.</p>
</div>
<div id="ref-ggplot2">
<p>Wickham, Hadley. 2009. <em>Ggplot2: Elegant Graphics for Data Analysis</em>. Springer-Verlag New York. <a href="http://ggplot2.org" class="uri">http://ggplot2.org</a>.</p>
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