Update site/NEWS

NEWS.md

@@ -8,22 +8,22 @@
 * Replace numerical indexing with name indexing for ```loadContigs()```
 * ```combineBCR()``` and ```combineTCR()``` no allow for unproductive contig inclusions with new **filterNonproductive** parameter.
 * ```combineBCR()``` will now prompt user if **samples** is not included instead of erroring.
-* Added base threshold by length for internal ```.lvcCmpare()```-
-* Ensured internal ```.lvcompare()``` only looks at first set of sequences in multi-sequence chain.
+* Added base threshold by length for internal ```.lvCompare()```
+* Ensured internal ```.lvCompare()``` only looks at first set of sequences in multi-sequence chain.
 * Fixed bug in exporting graph for ```clonaCluster()```
 * Fixed conflict in functions between igraph and dplyr packages
 
 # scRepertoire VERSION 2.0.2
 
 ## UNDERLYING CHANGES
 
-*```clonalOccupy()``` rewrite counting and NA handling
+* ```clonalOccupy()``` rewrite counting and NA handling
 
 # scRepertoire VERSION 2.0.1 
 
 ## UNDERLYING CHANGES
 
-*```clonalOverlay()``` arguments now cutpoint and use cut.category to select either clonalProportion or clonalFrequency
+* ```clonalOverlay()``` arguments now cutpoint and use cut.category to select either clonalProportion or clonalFrequency
 
 # scRepertoire VERSION 2.0.0 (2024-01-10)
 

inst/pkgdown.yml

@@ -18,7 +18,8 @@ articles:
   Running_Escape: Running_Escape.html
   SC_Visualizations: SC_Visualizations.html
   Trex: Trex.html
-last_built: 2024-02-24T16:17Z
+  vignette: vignette.html
+last_built: 2024-05-04T10:19Z
 urls:
   reference: https://www.borch.dev/uploads/scRepertoire/reference
   article: https://www.borch.dev/uploads/scRepertoire/articles

vignettes/articles/Running_Escape.Rmd

@@ -218,6 +218,15 @@ ggplot(data = as.data.frame(enrichment.scores),
   theme_classic() + 
   theme()
 ```
+Multi-core support is for all methods is available through [BiocParallel](https://bioconductor.org/packages/release/bioc/html/BiocParallel.html). To add more cores, use the argument **BPPARAM** to ```escape.matrix()```. Here we will use the ```SnowParam()``` for it's support across platforms and explicitly call 2 workers (or cores).
+
+```{r tidy=FALSE, eval=FALSE}
+enrichment.scores <- escape.matrix(scRep_example, 
+                                   gene.sets = GS.hallmark, 
+                                   groups = 5000, 
+                                   min.size = 5, 
+                                   BPPARAM = SnowParam(workers = 2))
+```
 
 ## runEscape
 
@@ -380,6 +389,7 @@ ridgeEnrichment(scRep_example,
                 assay = "escape.ssGSEA",
                 gene.set = "HALLMARK-IL2-STAT5-SIGNALING")
 ```
+
 We can get the relative position of individual cells along the x-axis using the **add.rug** parameter.
 
 ```{r tidy=FALSE}