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clonalQuant test vignette clonalBias parameters
BorchLab · Jan 10, 2024 · da5a22e · da5a22e
1 parent b593089
commit da5a22e
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Showing 4 changed files with 6 additions and 5 deletions.
diff --git a/R/clonalQuant.R b/R/clonalQuant.R
@@ -74,10 +74,10 @@ clonalQuant <- function(input.data,
   if (scale) { 
       y <- "scaled"
       mat$scaled <- mat$contigs/mat$total*100
-      ylab <- "Percent of Unique clone"
+      ylab <- "Percent of Unique Clones"
    } else { 
       y <- "contigs"
-      ylab <- "Unique Clonotypes"
+      ylab <- "Unique Clones"
    }
 
   if (exportTable) {

diff --git a/tests/testthat/_snaps/clonalQuant/clonalquant-scaled-plot.svg b/tests/testthat/_snaps/clonalQuant/clonalquant-scaled-plot.svg
diff --git a/tests/testthat/_snaps/clonalQuant/clonalquant-unscaled-plot.svg b/tests/testthat/_snaps/clonalQuant/clonalquant-unscaled-plot.svg
diff --git a/vignettes/vignette.Rmd b/vignettes/vignette.Rmd
@@ -1091,7 +1091,7 @@ clonalBias(scRep_example,
            split.by = "Patient", 
            group.by = "seurat_clusters",
            n.boots = 10, 
-           min.expand =5)
+           min.expand =0)
 ```
 
 ***
@@ -1170,6 +1170,7 @@ legend("topleft", legend = levels(color.legend), pch = 16, col = unique(col_samp
 ```
 
 ***
+
 # Conclusion  
 
 This has been a general overview of the capabilities of scRepertoire from the initial processing and visualization to attach to the mRNA expression values in a single-cell object. If you have any questions, comments, or suggestions, please visit the GitHub repository or [email me](mailto:ncborch@gmail.com).