Skip to content

Adding sort to gseaEnrichment levels #170

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
ncborcherding merged 1 commit into from
Jul 23, 2025
Merged

Adding sort to gseaEnrichment levels #170

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions R/gseaEnrichment.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand Down
5 changes: 3 additions & 2 deletions vignettes/escape.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
```

Expand Down Expand Up @@ -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).
Expand Down
Loading