Added ELBO plots to assess_fits_68k_pbmc analysis.

stephenslab · Jul 30, 2024 · e738719 · e738719
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diff --git a/analysis/examine_pbmc68k_more.R b/analysis/examine_pbmc68k_more.R
diff --git a/docs/assess_fits_68k_pbmc.html b/docs/assess_fits_68k_pbmc.html
diff --git a/docs/figure/assess_fits_68k_pbmc.Rmd/elbo-plots-1.png b/docs/figure/assess_fits_68k_pbmc.Rmd/elbo-plots-1.png
diff --git a/docs/figure/assess_fits_68k_pbmc.Rmd/loadings-scatterplot-k-12-1.png b/docs/figure/assess_fits_68k_pbmc.Rmd/loadings-scatterplot-k-12-1.png
diff --git a/docs/figure/assess_fits_68k_pbmc.Rmd/loadings-scatterplot-k-7-1.png b/docs/figure/assess_fits_68k_pbmc.Rmd/loadings-scatterplot-k-7-1.png
diff --git a/docs/figure/assess_fits_68k_pbmc.Rmd/plot-loglik-1.png b/docs/figure/assess_fits_68k_pbmc.Rmd/plot-loglik-1.png
diff --git a/docs/figure/assess_fits_68k_pbmc.Rmd/plot-loglik-vs-k-1.png b/docs/figure/assess_fits_68k_pbmc.Rmd/plot-loglik-vs-k-1.png
diff --git a/docs/figure/assess_fits_68k_pbmc.Rmd/plot-res-1.png b/docs/figure/assess_fits_68k_pbmc.Rmd/plot-res-1.png
diff --git a/docs/figure/assess_fits_68k_pbmc.Rmd/structure-plot-1.png b/docs/figure/assess_fits_68k_pbmc.Rmd/structure-plot-1.png
diff --git a/docs/figure/assess_fits_68k_pbmc.Rmd/structure-plot-em-1.png b/docs/figure/assess_fits_68k_pbmc.Rmd/structure-plot-em-1.png
diff --git a/docs/figure/assess_fits_68k_pbmc.Rmd/words-scatterplot-1.png b/docs/figure/assess_fits_68k_pbmc.Rmd/words-scatterplot-1.png
diff --git a/docs/site_libs/header-attrs-2.14/header-attrs.js b/docs/site_libs/header-attrs-2.14/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/site_libs/navigation-1.1/codefolding.js b/docs/site_libs/navigation-1.1/codefolding.js
@@ -31,7 +31,7 @@ window.initializeCodeFolding = function(show) {
     $(this).detach().appendTo(div);
 
     // add a show code button right above
-    var showCodeText = $('<span>' + (showThis ? 'Hide' : 'Show') + '</span>');
+    var showCodeText = $('<span>' + (showThis ? 'Hide' : 'Code') + '</span>');
     var showCodeButton = $('<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm code-folding-btn pull-right float-right"></button>');
     showCodeButton.append(showCodeText);
     showCodeButton
@@ -57,7 +57,7 @@ window.initializeCodeFolding = function(show) {
     //   * Change text
     //   * add a class for intermediate states styling
     div.on('hide.bs.collapse', function () {
-      showCodeText.text('Show');
+      showCodeText.text('Code');
       showCodeButton.addClass('btn-collapsing');
     });
     div.on('hidden.bs.collapse', function () {