diff --git a/articles/differential_signal_fixed_files/figure-html/plot-pca-1.png b/articles/differential_signal_fixed_files/figure-html/plot-pca-1.png
index 35fa6b3..352eb99 100644
Binary files a/articles/differential_signal_fixed_files/figure-html/plot-pca-1.png and b/articles/differential_signal_fixed_files/figure-html/plot-pca-1.png differ
diff --git a/pkgdown.yml b/pkgdown.yml
index 908d151..2b82c35 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,9 +1,9 @@
 pandoc: 3.1.1
 pkgdown: 2.0.7.9000
-pkgdown_sha: c9206802f2888992de92aa41f517ba7812f05331
+pkgdown_sha: 170015984ae234da3028b2b083df757227fdd241
 articles:
   differential_signal_fixed: differential_signal_fixed.html
   differential_signal_sliding: differential_signal_sliding.html
   range_based_functions: range_based_functions.html
-last_built: 2023-09-29T14:44Z
+last_built: 2023-09-30T17:02Z
 
diff --git a/reference/plotProfileHeatmap-methods.html b/reference/plotProfileHeatmap-methods.html
index 079f3fc..4d81b15 100644
--- a/reference/plotProfileHeatmap-methods.html
+++ b/reference/plotProfileHeatmap-methods.html
@@ -74,7 +74,7 @@ <h1>Draw a coverage Profile Heatmap</h1>
 <span><span class="co"># S4 method for GenomicRangesList</span></span>
 <span><span class="fu">plotProfileHeatmap</span><span class="op">(</span></span>
 <span>  <span class="va">object</span>,</span>
-<span>  <span class="va">profileCol</span>,</span>
+<span>  profileCol <span class="op">=</span> <span class="st">"profile_data"</span>,</span>
 <span>  xValue <span class="op">=</span> <span class="st">"bp"</span>,</span>
 <span>  fillValue <span class="op">=</span> <span class="st">"score"</span>,</span>
 <span>  facetX <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -86,13 +86,15 @@ <h1>Draw a coverage Profile Heatmap</h1>
 <span>  yLab <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  fillLab <span class="op">=</span> <span class="va">fillValue</span>,</span>
 <span>  relHeight <span class="op">=</span> <span class="fl">0.3</span>,</span>
+<span>  sortFilter <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  maxDist <span class="op">=</span> <span class="fl">100</span>,</span>
 <span>  <span class="va">...</span></span>
 <span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S4 method for GenomicRanges</span></span>
 <span><span class="fu">plotProfileHeatmap</span><span class="op">(</span></span>
 <span>  <span class="va">object</span>,</span>
-<span>  <span class="va">profileCol</span>,</span>
+<span>  profileCol <span class="op">=</span> <span class="st">"profile_data"</span>,</span>
 <span>  xValue <span class="op">=</span> <span class="st">"bp"</span>,</span>
 <span>  fillValue <span class="op">=</span> <span class="st">"score"</span>,</span>
 <span>  facetX <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -106,6 +108,8 @@ <h1>Draw a coverage Profile Heatmap</h1>
 <span>  relHeight <span class="op">=</span> <span class="fl">0.3</span>,</span>
 <span>  summaryLabelSide <span class="op">=</span> <span class="st">"left"</span>,</span>
 <span>  respectLevels <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  sortFilter <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  maxDist <span class="op">=</span> <span class="fl">100</span>,</span>
 <span>  <span class="va">...</span></span>
 <span><span class="op">)</span></span></code></pre></div>
     </div>
@@ -130,7 +134,7 @@ <h2>Arguments</h2>
 
 
 <dt>facetX, facetY</dt>
-<dd><p>Column used for facetting across the x- or y-axis
+<dd><p>Columns used for faceting across the x- or y-axis
 respectively</p></dd>
 
 
@@ -159,6 +163,21 @@ <h2>Arguments</h2>
 Represents the fraction of the plotting area taken up by the summary panel.</p></dd>
 
 
+<dt>sortFilter</dt>
+<dd><p>If calling on a GRangesList, a method for subsetting the
+original object (e.g. 1:2). If calling on a GRanges object should be and
+expression able to be parsed as a filtering expression using
+<a href="https://rlang.r-lib.org/reference/eval_tidy.html" class="external-link">eval_tidy</a>. This is applied when sorting the range order down
+the heatmap such that ranges can be sorted by one or specific samples, or
+all. Ranges will always be sorted such that those with the strongest signal
+are at the top of the plot</p></dd>
+
+
+<dt>maxDist</dt>
+<dd><p>Maximum distance from the centre to find the strongest signal
+when arranging the ranges</p></dd>
+
+
 <dt>summaryLabelSide</dt>
 <dd><p>Side to place y-axis for the summary plot in the top
 panel</p></dd>