https://github.com/alexvpickering/revigor
scrape REVIGO Gene Ontology web app and plot results
https://github.com/alexvpickering/revigor
gene-ontology microarray rna-seq
Last synced: 4 months ago
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scrape REVIGO Gene Ontology web app and plot results
- Host: GitHub
- URL: https://github.com/alexvpickering/revigor
- Owner: alexvpickering
- Created: 2020-07-18T01:17:50.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2021-03-17T00:50:06.000Z (almost 5 years ago)
- Last Synced: 2023-10-13T06:34:20.268Z (over 2 years ago)
- Topics: gene-ontology, microarray, rna-seq
- Language: R
- Homepage:
- Size: 2.68 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
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README
# revigoR
### Quickstart
```R
install.packages('remotes')
remotes::install_github('alexvpickering/revigoR')
library(revigoR)
# setup python virtualenv for scraping revigo (one time only)
setup_env()
# see ?add_path_genes for example workflow starting with limma differential expression
data(go_up1)
# submit goana result to revigo web app and download results to data_dir
data_dir <- tempdir()
scrape_revigo(data_dir, go_up1)
# forcegraph of revigo results (from cytoscape graph)
revigo_forcegraph(data_dir)
```
An interactive scatterplot using the MDS coordinate from revigo can also be generated:
```R
revigo_scatterplot(data_dir)
```
### Two GO Analyses
Visualize where revigo merges terms across two GO analyses (shades of purple) and doesn't (shades of orange and green for each analysis respectively):
```R
# two analyses
data(go_up2)
go_up1$analysis <- 0
go_up2$analysis <- 1
go_up <- rbind(go_up1, go_up2)
data_dir <- tempdir()
scrape_revigo(data_dir, go_up)
revigo_forcegraph(data_dir)
```
`revigo_scatterplot` also supports two analysis results:
```R
revigo_scatterplot(data_dir)
```
