my commit message

README.md

@@ -0,0 +1,12 @@
+# mPFC-web
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+The goal of mPFC-web is to show scRNAseq data and in situ data from our research!
+
+For more information, please enter our website: <gangcaolab.github.io/mPFC-web/>
+
+
+
+

docs/index.html

@@ -111,7 +111,8 @@
     <h2 id="toc-title">On this page</h2>
 
   <ul>
-  <li><a href="#barcode-image" id="toc-barcode-image" class="nav-link active" data-scroll-target="#barcode-image">Barcode image</a></li>
+  <li><a href="#scrnaseq-data" id="toc-scrnaseq-data" class="nav-link active" data-scroll-target="#scrnaseq-data">scRNAseq data</a></li>
+  <li><a href="#in-situ-data" id="toc-in-situ-data" class="nav-link" data-scroll-target="#in-situ-data">in situ data</a></li>
   </ul>
 </nav>
     </div>
@@ -147,13 +148,22 @@ <h1 class="title">mPFC-web</h1>
 
 </header>
 
-<section id="barcode-image" class="level1">
-<h1>Barcode image</h1>
+<section id="scrnaseq-data" class="level2">
+<h2 class="anchored" data-anchor-id="scrnaseq-data">scRNAseq data</h2>
 <p>This just a test!</p>
 <div class="cell">
 <div class="cell-output-display">
-<div id="htmlwidget-af17e577b95aaf073cd1" style="width:100%;height:480px;" class="vitessceR html-widget "></div>
-<script type="application/json" data-for="htmlwidget-af17e577b95aaf073cd1">{"x":{"config":{"version":"1.0.0","name":"Codeluppi et al., Nature Methods 2018","description":"","datasets":[{"uid":"A","name":"Codeluppi","files":[{"url":"https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/linnarsson/linnarsson.cells.json","type":"cells","fileType":"cells.json"},{"url":"https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/linnarsson/linnarsson.cell-sets.json","type":"cell-sets","fileType":"cell-sets.json"},{"url":"https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/linnarsson/linnarsson.molecules.json","type":"molecules","fileType":"molecules.json"},{"url":"https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/linnarsson/linnarsson.clusters.json","type":"expression-matrix","fileType":"clusters.json"},{"url":"https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/linnarsson/linnarsson.raster.json","type":"raster","fileType":"raster.json"}]}],"coordinationSpace":{"dataset":{"A":"A"},"embeddingType":{"A":"PCA","B":"t-SNE"}},"layout":[{"component":"description","coordinationScopes":{"dataset":"A"},"x":0,"y":0,"w":3,"h":3,"props":{"description":"Codeluppi et al., Nature Methods 2018: Spatial organization of the somatosensory cortex revealed by osmFISH."}},{"component":"spatial","coordinationScopes":{"dataset":"A"},"x":3,"y":6,"w":3,"h":6},{"component":"layerController","coordinationScopes":{"dataset":"A"},"x":0,"y":6,"w":3,"h":6},{"component":"scatterplot","coordinationScopes":{"dataset":"A","embeddingType":"A"},"x":6,"y":6,"w":3,"h":6},{"component":"scatterplot","coordinationScopes":{"dataset":"A","embeddingType":"B"},"x":6,"y":0,"w":3,"h":6},{"component":"status","coordinationScopes":{"dataset":"A"},"x":0,"y":3,"w":3,"h":3},{"component":"cellSets","coordinationScopes":{"dataset":"A"},"x":9,"y":6,"w":3,"h":6},{"component":"genes","coordinationScopes":{"dataset":"A"},"x":9,"y":0,"w":3,"h":6},{"component":"heatmap","coordinationScopes":{"dataset":"A"},"x":3,"y":0,"w":3,"h":6,"props":{"transpose":true}}],"initStrategy":"auto"},"theme":"light"},"evals":[],"jsHooks":[]}</script>
+<div id="htmlwidget-f78c2283e1f7f61f987a" style="width:100%;height:480px;" class="vitessceR html-widget "></div>
+<script type="application/json" data-for="htmlwidget-f78c2283e1f7f61f987a">{"x":{"config":{"version":"1.0.0","name":"Codeluppi et al., Nature Methods 2018","description":"","datasets":[{"uid":"A","name":"Codeluppi","files":[{"url":"https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/linnarsson/linnarsson.cells.json","type":"cells","fileType":"cells.json"},{"url":"https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/linnarsson/linnarsson.cell-sets.json","type":"cell-sets","fileType":"cell-sets.json"},{"url":"https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/linnarsson/linnarsson.molecules.json","type":"molecules","fileType":"molecules.json"},{"url":"https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/linnarsson/linnarsson.clusters.json","type":"expression-matrix","fileType":"clusters.json"},{"url":"https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/linnarsson/linnarsson.raster.json","type":"raster","fileType":"raster.json"}]}],"coordinationSpace":{"dataset":{"A":"A"},"embeddingType":{"A":"PCA","B":"t-SNE"}},"layout":[{"component":"description","coordinationScopes":{"dataset":"A"},"x":0,"y":0,"w":3,"h":3,"props":{"description":"Codeluppi et al., Nature Methods 2018: Spatial organization of the somatosensory cortex revealed by osmFISH."}},{"component":"spatial","coordinationScopes":{"dataset":"A"},"x":3,"y":6,"w":3,"h":6},{"component":"layerController","coordinationScopes":{"dataset":"A"},"x":0,"y":6,"w":3,"h":6},{"component":"scatterplot","coordinationScopes":{"dataset":"A","embeddingType":"A"},"x":6,"y":6,"w":3,"h":6},{"component":"scatterplot","coordinationScopes":{"dataset":"A","embeddingType":"B"},"x":6,"y":0,"w":3,"h":6},{"component":"status","coordinationScopes":{"dataset":"A"},"x":0,"y":3,"w":3,"h":3},{"component":"cellSets","coordinationScopes":{"dataset":"A"},"x":9,"y":6,"w":3,"h":6},{"component":"genes","coordinationScopes":{"dataset":"A"},"x":9,"y":0,"w":3,"h":6},{"component":"heatmap","coordinationScopes":{"dataset":"A"},"x":3,"y":0,"w":3,"h":6,"props":{"transpose":true}}],"initStrategy":"auto"},"theme":"light"},"evals":[],"jsHooks":[]}</script>
+</div>
+</div>
+</section>
+<section id="in-situ-data" class="level2">
+<h2 class="anchored" data-anchor-id="in-situ-data">in situ data</h2>
+<div class="cell">
+<div class="cell-output-display">
+<div id="htmlwidget-3cd29fa6e7b6eeda54b4" style="width:100%;height:480px;" class="vitessceR html-widget "></div>
+<script type="application/json" data-for="htmlwidget-3cd29fa6e7b6eeda54b4">{"x":{"config":{"version":"1.0.0","name":"My config","description":"","datasets":[{"uid":"A","name":"My dataset","files":[{"type":"raster","fileType":"raster.json","options":{"schemaVersion":"0.0.2","images":[{"name":"My Image","type":"ome-tiff","url":"https://vitessce-demo-data.storage.googleapis.com/exemplar-001/exemplar-001.pyramid.ome.tif"}],"renderLayers":["My Image"]}}]}],"coordinationSpace":{"dataset":{"A":"A"}},"layout":[{"component":"spatial","coordinationScopes":{"dataset":"A"},"x":0,"y":0,"w":6,"h":12},{"component":"layerController","coordinationScopes":{"dataset":"A"},"x":6,"y":0,"w":3,"h":12},{"component":"status","coordinationScopes":{"dataset":"A"},"x":9,"y":6,"w":3,"h":6},{"component":"description","coordinationScopes":{"dataset":"A"},"x":9,"y":0,"w":3,"h":6,"props":{"description":"Visualization of an OME-TIFF file."}}],"initStrategy":"auto"},"theme":"light"},"evals":[],"jsHooks":[]}</script>
 </div>
 </div>
 

docs/search.json

@@ -4,13 +4,27 @@
     "href": "index.html",
     "title": "mPFC-web",
     "section": "",
-    "text": "Barcode image\nThis just a test!"
+    "text": "This just a test!"
   },
   {
     "objectID": "about.html",
     "href": "about.html",
     "title": "About",
     "section": "",
     "text": "About this site\n\n1 + 1\n\n[1] 2"
+  },
+  {
+    "objectID": "index.html#scrnaseq-data",
+    "href": "index.html#scrnaseq-data",
+    "title": "mPFC-web",
+    "section": "",
+    "text": "This just a test!"
+  },
+  {
+    "objectID": "index.html#in-situ-data",
+    "href": "index.html#in-situ-data",
+    "title": "mPFC-web",
+    "section": "in situ data",
+    "text": "in situ data"
   }
 ]

index.qmd

@@ -5,8 +5,7 @@ date: 2023.07.12
 ---
 
 
-
-# Barcode image
+## scRNAseq data
 
 This just a test!
 
@@ -74,8 +73,54 @@ vc$widget(theme = "light", width = "100%")
 
 
 
+## in situ data
+
+```{r}
+#| echo: false
+
+library(vitessceR)
+
+# Define the image file options object.
+file_options = obj_list(
+  schemaVersion = "0.0.2",
+  images = list(
+      obj_list(
+        name = "My Image",
+        type = "ome-tiff",
+        url = "https://vitessce-demo-data.storage.googleapis.com/exemplar-001/exemplar-001.pyramid.ome.tif"
+      )
+  ),
+  renderLayers = list(
+    "My Image"
+  )
+)
+
+# Create Vitessce view config
+vc <- VitessceConfig$new("My config")
+dataset <- vc$add_dataset("My dataset")$add_file(
+  data_type = DataType$RASTER,
+  file_type = FileType$RASTER_JSON,
+  options = file_options
+)
+spatial <- vc$add_view(dataset, Component$SPATIAL)
+spatial_layers <- vc$add_view(dataset, Component$LAYER_CONTROLLER)
+status <- vc$add_view(dataset, Component$STATUS)
+desc <- vc$add_view(dataset, Component$DESCRIPTION)
+desc <- desc$set_props(description = "Visualization of an OME-TIFF file.")
+vc$layout(hconcat(
+  spatial,
+  hconcat(spatial_layers, vconcat(desc, status))
+))
+```
+
 
+```{r}
+#| message: false
+#| echo: false
 
+# Render the Vitessce widget
+vc$widget(theme = "light", width = "100%")
+```