Merge pull request #170 from BorchLab/ordering_correction

Adding sort to gseaEnrichment levels

Author: ncborcherding

R/gseaEnrichment.R

@@ -151,9 +151,9 @@ gseaEnrichment <- function(input.data,
   labNES <- formatC(nes, digits = digits, format = "f")
   labP   <- ifelse(is.na(pval), "NA",
                    formatC(pval, digits = 2, format = "e"))
-  pretty.grp <- paste0(groups,
+  pretty.grp <- sort(paste0(groups,
                        " (NES = ", labNES,
-                       ", p = ", labP, ")")
+                       ", p = ", labP, ")"))
 
   ## ---- 4.  Data frames for ggplot ------------------------------------------
   running.df <- data.frame(

vignettes/escape.Rmd

@@ -21,7 +21,7 @@ vignette: >
 ---
 
 ```{r, echo=FALSE, results="hide", message=FALSE}
-knitr::opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE)
+knitr::opts_chunk$set(tidy=FALSE, error=FALSE, message=FALSE, warning=FALSE)
 library(BiocStyle)
 ```
 
@@ -195,7 +195,8 @@ ggplot(data = as.data.frame(enrichment.scores),
       mapping = aes(enrichment.scores[,1], enrichment.scores[,2])) + 
   geom_point() + 
   theme_classic() + 
-  theme(axis.title = element_blank())
+  xlab(colnames(enrichment.scores)[1]) + 
+  ylab(colnames(enrichment.scores)[2]) 
 ```
 
 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).