🎨 rename marginal to pairwise

Wytamma · Apr 4, 2022 · d26530c · d26530c
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diff --git a/backend/beastiary/webapp-dist/index.html b/backend/beastiary/webapp-dist/index.html
@@ -1,3 +1,3 @@
 <!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"><!--[if IE]><link rel="icon" href="/favicon.ico"><![endif]--><title>Beastiary</title><link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,300,400,500,700,900"><link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Material+Icons"><link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,300,400,500,700,900"><link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Material+Icons"><link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,300,400,500,700,900"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/@mdi/font@latest/css/materialdesignicons.min.css"><style>html {
         overflow-y: auto !important;
-      }</style><link href="/css/login.4b7f13da.css" rel="prefetch"><link href="/css/login~main-dashboard.49552835.css" rel="prefetch"><link href="/css/login~main~main-dashboard.87cb79bc.css" rel="prefetch"><link href="/css/main-dashboard.21941226.css" rel="prefetch"><link href="/css/main.38cd41ea.css" rel="prefetch"><link href="/css/main~main-dashboard.27813474.css" rel="prefetch"><link href="/js/login.aa85044f.js" rel="prefetch"><link href="/js/login~main-dashboard.3ae3e551.js" rel="prefetch"><link href="/js/login~main~main-dashboard.3a1f6d10.js" rel="prefetch"><link href="/js/main-dashboard.5da8a2ea.js" rel="prefetch"><link href="/js/main.5136f4ee.js" rel="prefetch"><link href="/js/main~main-dashboard.80ebc61e.js" rel="prefetch"><link href="/js/reset-password.fe1c5ee2.js" rel="prefetch"><link href="/js/start.4abc32f1.js" rel="prefetch"><link href="/css/chunk-vendors.5b404c1b.css" rel="preload" as="style"><link href="/js/app.4a6cbf8f.js" rel="preload" as="script"><link href="/js/chunk-vendors.9a0991d8.js" rel="preload" as="script"><link href="/css/chunk-vendors.5b404c1b.css" rel="stylesheet"><link rel="icon" type="image/png" sizes="32x32" href="/img/icons/favicon-32x32.png"><link rel="icon" type="image/png" sizes="16x16" href="/img/icons/favicon-16x16.png"><link rel="manifest" href="/manifest.json"><meta name="theme-color" content="#4DBA87"><meta name="apple-mobile-web-app-capable" content="no"><meta name="apple-mobile-web-app-status-bar-style" content="default"><meta name="apple-mobile-web-app-title" content="frontend"><link rel="apple-touch-icon" href="/img/icons/apple-touch-icon-152x152.png"><link rel="mask-icon" href="/img/icons/safari-pinned-tab.svg" color="#4DBA87"><meta name="msapplication-TileImage" content="/img/icons/msapplication-icon-144x144.png"><meta name="msapplication-TileColor" content="#000000"></head><body><noscript><strong>We're sorry but Beastiary doesn't work properly without JavaScript enabled. Please enable it to continue.</strong></noscript><div id="app"></div><script src="/js/chunk-vendors.9a0991d8.js"></script><script src="/js/app.4a6cbf8f.js"></script></body></html>
+      }</style><link href="/css/login.4b7f13da.css" rel="prefetch"><link href="/css/login~main-dashboard.49552835.css" rel="prefetch"><link href="/css/login~main~main-dashboard.87cb79bc.css" rel="prefetch"><link href="/css/main-dashboard.21941226.css" rel="prefetch"><link href="/css/main.38cd41ea.css" rel="prefetch"><link href="/css/main~main-dashboard.27813474.css" rel="prefetch"><link href="/js/login.aa85044f.js" rel="prefetch"><link href="/js/login~main-dashboard.3ae3e551.js" rel="prefetch"><link href="/js/login~main~main-dashboard.3a1f6d10.js" rel="prefetch"><link href="/js/main-dashboard.06a298e8.js" rel="prefetch"><link href="/js/main.5136f4ee.js" rel="prefetch"><link href="/js/main~main-dashboard.80ebc61e.js" rel="prefetch"><link href="/js/reset-password.fe1c5ee2.js" rel="prefetch"><link href="/js/start.4abc32f1.js" rel="prefetch"><link href="/css/chunk-vendors.5b404c1b.css" rel="preload" as="style"><link href="/js/app.3a8a8e57.js" rel="preload" as="script"><link href="/js/chunk-vendors.9a0991d8.js" rel="preload" as="script"><link href="/css/chunk-vendors.5b404c1b.css" rel="stylesheet"><link rel="icon" type="image/png" sizes="32x32" href="/img/icons/favicon-32x32.png"><link rel="icon" type="image/png" sizes="16x16" href="/img/icons/favicon-16x16.png"><link rel="manifest" href="/manifest.json"><meta name="theme-color" content="#4DBA87"><meta name="apple-mobile-web-app-capable" content="no"><meta name="apple-mobile-web-app-status-bar-style" content="default"><meta name="apple-mobile-web-app-title" content="frontend"><link rel="apple-touch-icon" href="/img/icons/apple-touch-icon-152x152.png"><link rel="mask-icon" href="/img/icons/safari-pinned-tab.svg" color="#4DBA87"><meta name="msapplication-TileImage" content="/img/icons/msapplication-icon-144x144.png"><meta name="msapplication-TileColor" content="#000000"></head><body><noscript><strong>We're sorry but Beastiary doesn't work properly without JavaScript enabled. Please enable it to continue.</strong></noscript><div id="app"></div><script src="/js/chunk-vendors.9a0991d8.js"></script><script src="/js/app.3a8a8e57.js"></script></body></html>
diff --git a/.../beastiary/webapp-dist/js/app.4a6cbf8f.js → .../beastiary/webapp-dist/js/app.3a8a8e57.js b/.../beastiary/webapp-dist/js/app.4a6cbf8f.js → .../beastiary/webapp-dist/js/app.3a8a8e57.js
diff --git a/...stiary/webapp-dist/js/app.4a6cbf8f.js.map → ...stiary/webapp-dist/js/app.3a8a8e57.js.map b/...stiary/webapp-dist/js/app.4a6cbf8f.js.map → ...stiary/webapp-dist/js/app.3a8a8e57.js.map
diff --git a/...webapp-dist/js/main-dashboard.5da8a2ea.js → ...webapp-dist/js/main-dashboard.06a298e8.js b/...webapp-dist/js/main-dashboard.5da8a2ea.js → ...webapp-dist/js/main-dashboard.06a298e8.js
diff --git a/...pp-dist/js/main-dashboard.5da8a2ea.js.map → ...pp-dist/js/main-dashboard.06a298e8.js.map b/...pp-dist/js/main-dashboard.5da8a2ea.js.map → ...pp-dist/js/main-dashboard.06a298e8.js.map
diff --git a/...ifest.cb6f36d74a3ef3040abcbe4f5292a63a.js → ...ifest.17317f514f7278a37554b3d83f96538f.js b/...ifest.cb6f36d74a3ef3040abcbe4f5292a63a.js → ...ifest.17317f514f7278a37554b3d83f96538f.js
@@ -16,7 +16,7 @@ self.__precacheManifest = (self.__precacheManifest || []).concat([
     "url": "/css/login~main~main-dashboard.87cb79bc.css"
   },
   {
-    "revision": "727ece419e943fd914c3",
+    "revision": "06cd3ff32f227a397e22",
     "url": "/css/main-dashboard.21941226.css"
   },
   {
@@ -28,12 +28,12 @@ self.__precacheManifest = (self.__precacheManifest || []).concat([
     "url": "/css/main~main-dashboard.27813474.css"
   },
   {
-    "revision": "a4659610f56ef2aebc70032e32beb209",
+    "revision": "401484f6e6d72ce76a6cab96076b28dd",
     "url": "/index.html"
   },
   {
-    "revision": "00bd310ed85065f3c67c",
-    "url": "/js/app.4a6cbf8f.js"
+    "revision": "22b3d26ccaa3850251de",
+    "url": "/js/app.3a8a8e57.js"
   },
   {
     "revision": "efb27178083e9bac70b9",
@@ -52,8 +52,8 @@ self.__precacheManifest = (self.__precacheManifest || []).concat([
     "url": "/js/login~main~main-dashboard.3a1f6d10.js"
   },
   {
-    "revision": "727ece419e943fd914c3",
-    "url": "/js/main-dashboard.5da8a2ea.js"
+    "revision": "06cd3ff32f227a397e22",
+    "url": "/js/main-dashboard.06a298e8.js"
   },
   {
     "revision": "22a0af3690e2a870c9ae",

diff --git a/backend/beastiary/webapp-dist/service-worker.js b/backend/beastiary/webapp-dist/service-worker.js
@@ -14,7 +14,7 @@
 importScripts("https://storage.googleapis.com/workbox-cdn/releases/4.3.1/workbox-sw.js");
 
 importScripts(
-  "/precache-manifest.cb6f36d74a3ef3040abcbe4f5292a63a.js"
+  "/precache-manifest.17317f514f7278a37554b3d83f96538f.js"
 );
 
 workbox.core.setCacheNameDetails({prefix: "frontend"});

diff --git a/backend/pyproject.toml b/backend/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "beastiary"
-version = "1.5.2"
+version = "1.5.3"
 description = ""
 authors = ["Wytamma Wirth <[email protected]>"]
 readme = "PYPI-README.md"

diff --git a/docs/images/marginal.png → docs/images/pairwise.png b/docs/images/marginal.png → docs/images/pairwise.png
diff --git a/docs/plots/joint-marginal.md b/docs/plots/joint-marginal.md
diff --git a/docs/plots/pairwise.md b/docs/plots/pairwise.md
@@ -0,0 +1,5 @@
+The 'Pairwise' panel will pairwise plots for the selected traces. Pairwise plots are useful for finding correlations between the samples.
+
+![](../images/pairwise.png)
+
+Here we can see that `meanRate` is negatively correlated with `treeLength`.
diff --git a/docs/tutorial/google-colab.md b/docs/tutorial/google-colab.md
@@ -4,4 +4,4 @@ For example, beastiary can be run in Google Colab notebooks. [Enzo Andree](https
 
 Here you can see an example of this notebook adapted to also run beastiary: 
 
-[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Wytamma/ColabBEAST/blob/main/BEAST2.ipynb)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1XfKBhTLIenFUB1_uoDwKBnJey6gHna4e?usp=sharing)
diff --git a/...d/src/components/data/graphs/Marginal.vue → ...d/src/components/data/graphs/Pairwise.vue b/...d/src/components/data/graphs/Marginal.vue → ...d/src/components/data/graphs/Pairwise.vue
@@ -1,6 +1,6 @@
 <template>
     <Plotly :data="JointData" :layout="layout" :toImageButtonOptions="{
-          filename: 'marginal',
+          filename: 'pairwise',
           width: null,
           height: null,
           format: 'svg'
@@ -19,7 +19,7 @@ import { Component, Vue } from 'vue-property-decorator';
   },
 })
 // @ts-ignore
-export default class Marginal extends Vue {
+export default class Pairwise extends Vue {
     get modeBarButtons() {
       return [
         'zoom2d', 'pan2d', 'select2d', 'lasso2d', 'zoomIn2d', 'zoomOut2d', 'autoScale2d', 'resetScale2d',

diff --git a/frontend/src/views/main/Dashboard.vue b/frontend/src/views/main/Dashboard.vue
@@ -34,7 +34,7 @@
                   Histogram
                 </v-tab>
                 <v-tab>
-                  Marginal
+                  Pairwise
                 </v-tab>
                 <v-tab>
                   Parallel
@@ -64,7 +64,7 @@
               </v-tab-item>
               <v-tab-item>
                 <v-card flat class="pa-2"  fill-height>
-                    <Marginal v-if="tab === 3"/>
+                    <Pairwise v-if="tab === 3"/>
                 </v-card>
               </v-tab-item>
               <v-tab-item>
@@ -97,7 +97,7 @@ import '@/assets/css/custom.css';
 import AddTraceButton from '@/components/data/AddTraceButton.vue';
 import CumulativeESS from '@/components/data/graphs/ESS.vue';
 import Histogram from '@/components/data/graphs/Histogram.vue';
-import Marginal from '@/components/data/graphs/Marginal.vue';
+import Pairwise from '@/components/data/graphs/Pairwise.vue';
 import Parallel from '@/components/data/graphs/Parallel.vue';
 import Trace from '@/components/data/graphs/Trace.vue';
 import Violin from '@/components/data/graphs/Violin.vue';
@@ -122,7 +122,7 @@ import { Component, Vue } from 'vue-property-decorator';
     AddTraceButton,
     StatsTable,
     CumulativeESS,
-    Marginal,
+    Pairwise,
   },
 })
 export default class Dashboard extends Vue {

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -18,7 +18,7 @@ nav:
   - tutorial/google-colab.md
   - tutorial/running-in-the-background.md
 - Plots:
-  - plots/joint-marginal.md
+  - plots/pairwise.md
   - plots/Cumulative-ESS.md
   - plots/parallel-coordinates.md
 - Design and Implementation: design.md
Original file line number	Diff line number	Diff line change
Expand Up		@@ -4,4 +4,4 @@ For example, beastiary can be run in Google Colab notebooks. [Enzo Andree](https

		Here you can see an example of this notebook adapted to also run beastiary:

		[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Wytamma/ColabBEAST/blob/main/BEAST2.ipynb)
		[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1XfKBhTLIenFUB1_uoDwKBnJey6gHna4e?usp=sharing)