Merge pull request #186 from Artur-man/main

update niche clustering tutorial and fix a bug in hot spot analysis
BIMSBbioinfo · Jan 2, 2025 · 5cd62f3 · 5cd62f3
2 parents 2964682 + 40f2332
commit 5cd62f3
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Showing 19 changed files with 204 additions and 114 deletions.
diff --git a/R/spatial.R b/R/spatial.R
@@ -355,6 +355,7 @@ getHotSpotAnalysis <- function(object, assay = NULL, method = "Getis-Ord", featu
 
         # calculate getis ord
         n <- length(statistic)
+        statistic <- statistic - (min(statistic)) ### correct for negative scores, correct for this later
         getisord_stat <- adj_matrix %*% statistic
         getisord_stat <- getisord_stat/(sum(statistic) - statistic)
         getisord[[1]] <- getisord_stat[,1]

diff --git a/docs/_site.yml b/docs/_site.yml
@@ -14,7 +14,7 @@ navbar:
         - text: "Multi-omic Integration"
           href: multiomic.html
         - text: "Niche Clustering"
-          href: deconvolution.html
+          href: nicheclustering.html
       - text: "Downstream Analysis"
         menu:
         - text: "ROI Analysis"

diff --git a/docs/conversion.html b/docs/conversion.html
@@ -346,7 +346,7 @@
           <a href="multiomic.html">Multi-omic Integration</a>
         </li>
         <li>
-          <a href="deconvolution.html">Niche Clustering</a>
+          <a href="nicheclustering.html">Niche Clustering</a>
         </li>
       </ul>
     </li>

diff --git a/docs/importingdata.html b/docs/importingdata.html
@@ -346,7 +346,7 @@
           <a href="multiomic.html">Multi-omic Integration</a>
         </li>
         <li>
-          <a href="deconvolution.html">Niche Clustering</a>
+          <a href="nicheclustering.html">Niche Clustering</a>
         </li>
       </ul>
     </li>

diff --git a/docs/index.html b/docs/index.html
@@ -264,7 +264,7 @@
           <a href="multiomic.html">Multi-omic Integration</a>
         </li>
         <li>
-          <a href="deconvolution.html">Niche Clustering</a>
+          <a href="nicheclustering.html">Niche Clustering</a>
         </li>
       </ul>
     </li>

diff --git a/docs/interactive.Rmd b/docs/interactive.Rmd
@@ -37,7 +37,7 @@ knitr::opts_chunk$set(highlight = TRUE, echo = TRUE)
 
 # Interactive Annotation
 
-**VoltRon** includes interactive applications to select and manually label spatial points by drawing polygons and circles. As an example, we will use a Spot-based spatial transcriptomic assay, specifically the **Mouse Brain Serial Section 1/2** datasets, analyzed in the [Niche Clustering](deconvolution.html) tutorial. You can find the already analyzed data stored as a VoltRon object [here](https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/NicheClustering/Visium&Visium_data_decon_analyzed.rds)
+**VoltRon** includes interactive applications to select and manually label spatial points by drawing polygons and circles. As an example, we will use a Spot-based spatial transcriptomic assay, specifically the **Mouse Brain Serial Section 1/2** datasets, analyzed in the [Niche Clustering](nicheclustering.html) tutorial. You can find the already analyzed data stored as a VoltRon object [here](https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/NicheClustering/Visium&Visium_data_decon_analyzed.rds)
 
 ```{r class.source="watch-out", eval = FALSE}
 MBrain_Sec <- readRDS("Visium&Visium_data_decon_analyzed.rds")

diff --git a/docs/interactive.html b/docs/interactive.html
@@ -346,7 +346,7 @@
           <a href="multiomic.html">Multi-omic Integration</a>
         </li>
         <li>
-          <a href="deconvolution.html">Niche Clustering</a>
+          <a href="nicheclustering.html">Niche Clustering</a>
         </li>
       </ul>
     </li>
@@ -464,7 +464,7 @@ <h1>Interactive Annotation</h1>
 and manually label spatial points by drawing polygons and circles. As an
 example, we will use a Spot-based spatial transcriptomic assay,
 specifically the <strong>Mouse Brain Serial Section 1/2</strong>
-datasets, analyzed in the <a href="deconvolution.html">Niche
+datasets, analyzed in the <a href="nicheclustering.html">Niche
 Clustering</a> tutorial. You can find the already analyzed data stored
 as a VoltRon object <a
 href="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/NicheClustering/Visium&amp;Visium_data_decon_analyzed.rds">here</a></p>

diff --git a/docs/moleculeanalysis.html b/docs/moleculeanalysis.html
@@ -346,7 +346,7 @@
           <a href="multiomic.html">Multi-omic Integration</a>
         </li>
         <li>
-          <a href="deconvolution.html">Niche Clustering</a>
+          <a href="nicheclustering.html">Niche Clustering</a>
         </li>
       </ul>
     </li>

diff --git a/docs/multiomic.html b/docs/multiomic.html
@@ -346,7 +346,7 @@
           <a href="multiomic.html">Multi-omic Integration</a>
         </li>
         <li>
-          <a href="deconvolution.html">Niche Clustering</a>
+          <a href="nicheclustering.html">Niche Clustering</a>
         </li>
       </ul>
     </li>

diff --git a/docs/deconvolution.Rmd → docs/nicheclustering.Rmd b/docs/deconvolution.Rmd → docs/nicheclustering.Rmd
diff --git a/docs/deconvolution.html → docs/nicheclustering.html b/docs/deconvolution.html → docs/nicheclustering.html
diff --git a/docs/ondisk.html b/docs/ondisk.html
@@ -346,7 +346,7 @@
           <a href="multiomic.html">Multi-omic Integration</a>
         </li>
         <li>
-          <a href="deconvolution.html">Niche Clustering</a>
+          <a href="nicheclustering.html">Niche Clustering</a>
         </li>
       </ul>
     </li>

diff --git a/docs/pixelanalysis.html b/docs/pixelanalysis.html
@@ -346,7 +346,7 @@
           <a href="multiomic.html">Multi-omic Integration</a>
         </li>
         <li>
-          <a href="deconvolution.html">Niche Clustering</a>
+          <a href="nicheclustering.html">Niche Clustering</a>
         </li>
       </ul>
     </li>

diff --git a/docs/registration.html b/docs/registration.html
@@ -346,7 +346,7 @@
           <a href="multiomic.html">Multi-omic Integration</a>
         </li>
         <li>
-          <a href="deconvolution.html">Niche Clustering</a>
+          <a href="nicheclustering.html">Niche Clustering</a>
         </li>
       </ul>
     </li>

diff --git a/docs/roianalysis.html b/docs/roianalysis.html
@@ -346,7 +346,7 @@
           <a href="multiomic.html">Multi-omic Integration</a>
         </li>
         <li>
-          <a href="deconvolution.html">Niche Clustering</a>
+          <a href="nicheclustering.html">Niche Clustering</a>
         </li>
       </ul>
     </li>

diff --git a/docs/spotanalysis.html b/docs/spotanalysis.html
@@ -346,7 +346,7 @@
           <a href="multiomic.html">Multi-omic Integration</a>
         </li>
         <li>
-          <a href="deconvolution.html">Niche Clustering</a>
+          <a href="nicheclustering.html">Niche Clustering</a>
         </li>
       </ul>
     </li>

diff --git a/docs/tutorials.Rmd b/docs/tutorials.Rmd
@@ -72,7 +72,7 @@ In addition, VoltRon provides a number of spatially aware data analysis methods
       <img width="80%" height="80%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/multiomic.png" class="center">
       <p style = "margin: 3%"> Integrating data modalities within or across tissue sections </p>
    </td>
-   <td onclick="location.href='deconvolution.html';"> 
+   <td onclick="location.href='nicheclustering.html';"> 
       <p class ="tutorial"> Niche Clustering </p>
       <img width="80%" height="80%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/deconvolution.png" class="center">
       <p style = "margin: 5%"> Clustering based on ROI/spot deconvolution and Spatial Neighborhood </p>

diff --git a/docs/tutorials.html b/docs/tutorials.html
@@ -264,7 +264,7 @@
           <a href="multiomic.html">Multi-omic Integration</a>
         </li>
         <li>
-          <a href="deconvolution.html">Niche Clustering</a>
+          <a href="nicheclustering.html">Niche Clustering</a>
         </li>
       </ul>
     </li>
@@ -444,7 +444,7 @@ <h2>Spatially Aware Data Integration and Analysis</h2>
 Integrating data modalities within or across tissue sections
 </p>
 </td>
-<td onclick="location.href=&#39;deconvolution.html&#39;;">
+<td onclick="location.href=&#39;nicheclustering.html&#39;;">
 <p class="tutorial">
 Niche Clustering
 </p>

diff --git a/docs/voltronobjects.html b/docs/voltronobjects.html
@@ -346,7 +346,7 @@
           <a href="multiomic.html">Multi-omic Integration</a>
         </li>
         <li>
-          <a href="deconvolution.html">Niche Clustering</a>
+          <a href="nicheclustering.html">Niche Clustering</a>
         </li>
       </ul>
     </li>
-Original file line number
+Diff line change
@@ Expand Up / @@ -346,7 +346,7 @@ @@
               <a href="multiomic.html">Multi-omic Integration</a>
             </li>
             <li>
-              <a href="deconvolution.html">Niche Clustering</a>
+              <a href="nicheclustering.html">Niche Clustering</a>
             </li>
           </ul>
         </li>
@@ Expand Down @@