Merge remote branch

Merge branch 'main' of github.com:fmicompbio/intermediate_ggplot2

# Conflicts:
#	3_many_points_scatterplot.html

Author: csoneson

3_many_points_scatterplot.html

@@ -3181,12 +3181,12 @@ <h3 class="anchored" data-anchor-id="plot">Plot</h3>
 <p>Let’s first create a simple scatter plot to illustrate the problems. The <code>diamonds</code> dataset has 53940 observations. If stored into a vectorized graphics device such as <code>pdf()</code> or <code>svg()</code>, the file will be large (each observation is individually represented as graphic elements) and slow to open or arrange. Furthermore, the high number of data points leads to saturation and we do not see the full underlying density of data points.</p>
 <div class="cell">
 <div class="sourceCode cell-code" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="co"># create base plot</span></span>
-<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>p0 <span class="ot">&lt;-</span> <span class="fu">ggplot</span>(<span class="at">data =</span> diamonds, <span class="at">mapping =</span> <span class="fu">aes</span>(<span class="at">x =</span> carat, <span class="at">y =</span> price)) <span class="sc">+</span></span>
+<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>gg <span class="ot">&lt;-</span> <span class="fu">ggplot</span>(<span class="at">data =</span> diamonds, <span class="at">mapping =</span> <span class="fu">aes</span>(<span class="at">x =</span> carat, <span class="at">y =</span> price)) <span class="sc">+</span></span>
 <span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>    <span class="fu">labs</span>(<span class="at">x =</span> <span class="st">&quot;Weight of the diamond (carat)&quot;</span>, <span class="at">y =</span> <span class="st">&quot;Price (US dollars)&quot;</span>) <span class="sc">+</span></span>
 <span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a>    <span class="fu">theme_bw</span>(<span class="dv">20</span>) <span class="sc">+</span></span>
 <span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a>    <span class="fu">theme</span>(<span class="at">panel.grid =</span> <span class="fu">element_blank</span>(),</span>
 <span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a>          <span class="at">legend.position =</span> <span class="st">&quot;bottom&quot;</span>)</span>
-<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a>p0 <span class="sc">+</span> <span class="fu">geom_point</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a>gg <span class="sc">+</span> <span class="fu">geom_point</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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 <figure class="figure">
@@ -3200,7 +3200,7 @@ <h3 class="anchored" data-anchor-id="plot">Plot</h3>
 <details class="code-fold">
 <summary>Code</summary>
 <div class="sourceCode cell-code" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="co"># ... with transparency</span></span>
-<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>p0 <span class="sc">+</span> <span class="fu">geom_point</span>(<span class="at">color =</span> <span class="fu">alpha</span>(<span class="st">&quot;black&quot;</span>, <span class="fl">0.02</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>gg <span class="sc">+</span> <span class="fu">geom_point</span>(<span class="at">color =</span> <span class="fu">alpha</span>(<span class="st">&quot;black&quot;</span>, <span class="fl">0.02</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 <div class="cell-output-display">
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@@ -3215,7 +3215,7 @@ <h3 class="anchored" data-anchor-id="plot">Plot</h3>
 <details class="code-fold">
 <summary>Code</summary>
 <div class="sourceCode cell-code" id="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="co"># ... with marginal density plots by number of cylinders</span></span>
-<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>p0 <span class="sc">+</span> <span class="fu">geom_density_2d_filled</span>(<span class="at">bins =</span> <span class="dv">48</span>) <span class="sc">+</span></span>
+<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>gg <span class="sc">+</span> <span class="fu">geom_density_2d_filled</span>(<span class="at">bins =</span> <span class="dv">48</span>) <span class="sc">+</span></span>
 <span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a>    <span class="fu">coord_cartesian</span>(<span class="at">expand =</span> <span class="cn">FALSE</span>) <span class="sc">+</span></span>
 <span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a>    <span class="fu">theme</span>(<span class="at">legend.position =</span> <span class="st">&quot;none&quot;</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
@@ -3227,12 +3227,12 @@ <h3 class="anchored" data-anchor-id="plot">Plot</h3>
 </div>
 </div>
 </div>
-<p>The linear contour levels or color intervals (controlled by <code>bins</code> or <code>breaks</code>) may not work well in a case like ours, where the density is very high in some regions that will occupy almost the complete color scale and we lose resoulution in low density regions. You can use <code>breaks</code> to create non-linear intervals (here combined with <code>ndensity</code> so that we know the range of densities: [0, 1]) and with <code>theme(panel.background)</code> to make the zero-density area dark blue.</p>
+<p>The linear contour levels or color intervals (controlled by <code>bins</code> or <code>breaks</code>) may not work well in a case like ours, where the density is very high in some regions that will occupy almost the complete color scale and we lose resolution in low density regions. You can use <code>breaks</code> to create non-linear intervals (here combined with <code>ndensity</code> so that we know the range of densities: [0, 1]) and with <code>theme(panel.background)</code> to make the zero-density area dark blue.</p>
 <div class="cell">
 <details class="code-fold">
 <summary>Code</summary>
 <div class="sourceCode cell-code" id="cb7"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="co"># ... with marginal density plots by number of cylinders</span></span>
-<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a>p0 <span class="sc">+</span> <span class="fu">geom_density_2d_filled</span>(<span class="at">contour_var =</span> <span class="st">&quot;ndensity&quot;</span>,</span>
+<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a>gg <span class="sc">+</span> <span class="fu">geom_density_2d_filled</span>(<span class="at">contour_var =</span> <span class="st">&quot;ndensity&quot;</span>,</span>
 <span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a>                            <span class="at">breaks =</span> <span class="fu">exp</span>(<span class="fu">seq</span>(<span class="fu">log</span>(<span class="fl">1e-4</span>), <span class="fu">log</span>(<span class="dv">1</span>), <span class="at">length.out =</span> <span class="dv">64</span>))) <span class="sc">+</span></span>
 <span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a>    <span class="fu">coord_cartesian</span>(<span class="at">expand =</span> <span class="cn">FALSE</span>) <span class="sc">+</span></span>
 <span id="cb7-5"><a href="#cb7-5" aria-hidden="true" tabindex="-1"></a>    <span class="fu">theme</span>(<span class="at">legend.position =</span> <span class="st">&quot;none&quot;</span>,</span>
@@ -3251,7 +3251,7 @@ <h3 class="anchored" data-anchor-id="plot">Plot</h3>
 <details class="code-fold">
 <summary>Code</summary>
 <div class="sourceCode cell-code" id="cb8"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="co"># ... with marginal violin and labelled data points</span></span>
-<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a>p0 <span class="sc">+</span> <span class="fu">geom_scattermore</span>(<span class="at">pointsize =</span> <span class="dv">2</span>, <span class="at">alpha =</span> <span class="fl">0.02</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a>gg <span class="sc">+</span> <span class="fu">geom_scattermore</span>(<span class="at">pointsize =</span> <span class="dv">2</span>, <span class="at">alpha =</span> <span class="fl">0.02</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 <div class="cell-output-display">
 <div>

3_many_points_scatterplot.qmd

@@ -65,12 +65,12 @@ leads to saturation and we do not see the full underlying density of data points
 #| code-fold: false
 
 # create base plot
-p0 <- ggplot(data = diamonds, mapping = aes(x = carat, y = price)) +
+gg <- ggplot(data = diamonds, mapping = aes(x = carat, y = price)) +
     labs(x = "Weight of the diamond (carat)", y = "Price (US dollars)") +
     theme_bw(20) +
     theme(panel.grid = element_blank(),
           legend.position = "bottom")
-p0 + geom_point()
+gg + geom_point()
 ```
 
 A simple way to improve the saturation issue is to use transparency, so that
@@ -83,7 +83,7 @@ solve the "many points" problem yet.
 #| fig-height: 7
 
 # ... with transparency
-p0 + geom_point(color = alpha("black", 0.02))
+gg + geom_point(color = alpha("black", 0.02))
 ```
 
 A simple way to solve also the "many points" problem is to avoid showing
@@ -96,14 +96,14 @@ using a color scale.
 #| fig-height: 7
 
 # ... with marginal density plots by number of cylinders
-p0 + geom_density_2d_filled(bins = 48) +
+gg + geom_density_2d_filled(bins = 48) +
     coord_cartesian(expand = FALSE) +
     theme(legend.position = "none")
 ```
 
 The linear contour levels or color intervals (controlled by `bins` or `breaks`)
 may not work well in a case like ours, where the density is very high in some
-regions that will occupy almost the complete color scale and we lose resoulution
+regions that will occupy almost the complete color scale and we lose resolution
 in low density regions. You can use `breaks` to create non-linear intervals
 (here combined with `ndensity` so that we know the range of densities: [0, 1])
 and with `theme(panel.background)` to make the zero-density area dark blue.
@@ -114,7 +114,7 @@ and with `theme(panel.background)` to make the zero-density area dark blue.
 #| fig-height: 7
 
 # ... with marginal density plots by number of cylinders
-p0 + geom_density_2d_filled(contour_var = "ndensity",
+gg + geom_density_2d_filled(contour_var = "ndensity",
                             breaks = exp(seq(log(1e-4), log(1), length.out = 64))) +
     coord_cartesian(expand = FALSE) +
     theme(legend.position = "none",
@@ -131,7 +131,7 @@ hard to use, `scattermore` provides a solution for that too.
 #| fig-height: 7
 
 # ... with marginal violin and labelled data points
-p0 + geom_scattermore(pointsize = 2, alpha = 0.02)
+gg + geom_scattermore(pointsize = 2, alpha = 0.02)
 ```