Add diffSCESets to vignette

R/compare.R

@@ -219,12 +219,11 @@ compareSCESets <- function(sces) {
 #' @examples
 #' sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
 #' sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
-#' comparison <- compareSCESets(list(Splat = sim1, Simple = sim2))
-#' names(comparison)
-#' names(comparison$Plots)
-#' @importFrom ggplot2 ggplot aes_string geom_point geom_smooth geom_boxplot
-#' geom_violin scale_y_continuous scale_y_log10 scale_x_log10 xlab ylab ggtitle
-#' theme_minimal
+#' difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
+#' names(difference)
+#' names(difference$Plots)
+#' @importFrom ggplot2 ggplot aes_string geom_point geom_boxplot xlab ylab
+#' ggtitle theme_minimal
 #' @importFrom scater cpm<-
 #' @export
 diffSCESets <- function(sces, ref) {

man/diffSCESets.Rd

@@ -70,7 +70,7 @@ using \code{\link[ggplot2]{ggplot}}.
 \examples{
 sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
 sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
-comparison <- compareSCESets(list(Splat = sim1, Simple = sim2))
-names(comparison)
-names(comparison$Plots)
+difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
+names(difference)
+names(difference$Plots)
 }

vignettes/splatter.Rmd

@@ -452,6 +452,27 @@ ggplot(comparison$PhenoData,
     geom_point()
 ```
 
+## Comparing differences
+
+Sometimes instead of visually comparing datasets it may be more interesting to
+look at the differences between them. We can do this using the `diffSCESets`
+function. Similar to `compareSCESets` this function takes a list of `SCESet`
+objects but now we also specify one to be a reference. A series of similar plots
+are returned but instead of showing the overall distributions they demonstrate
+differences from the reference.
+
+```{r difference}
+difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
+difference$Plots$Means
+```
+
+We also get a series of Quantile-Quantile plot that can be used to compare
+distributions.
+
+```{r difference-qq}
+difference$QQPlots$Means
+```
+
 # Session information {-}
 
 ```{r sessionInfo}