revigo_scatterplot: Revigo MDS plot
In alexvpickering/revigoR: Scrape revigo webapp and plot results

Description Usage Arguments Details Value Examples

Uses MDS coordinates from revigo.

1	revigo_scatterplot(data_dir)

data_dir

directory with scraped revigo data

If add_path_genes is called, hovering a node will show the logFC of significant genes in all GO terms merged into the representative GO term in question. At most 70 upregulated (red) and 70 downregulated (blue) genes with the largest absolute logFC are displayed. If scrape_revigo is used with two analyses (see examples), revigo ontolgies where no merge occured across analyses will be shades of orange (analysis 0) and green (analysis 1) while ontologies where a merge occured across analyses will be shades of purple. For tooltip heatmaps with two analyses, the 70 up-regulated genes shown are up in the analysis of the hovered node (analysis 0 for merged nodes), prioritizing the inclusion of genes differentially expressed in both analyses. The 70 down-regulated genes shown are chosen similarly.

r2d3 plot

# single analysis
data(go_up1)
data_dir <- tempdir()
scrape_revigo(data_dir, go_up1)
revigo_scatterplot(data_dir)

# two analyses
data(go_up2)
data_dir <- tempdir()
go_up1$analysis <- 0
go_up2$analysis <- 1
go_up <- rbind(go_up1, go_up2)
scrape_revigo(data_dir, go_up)
revigo_scatterplot(data_dir)