revigo_forcegraph: Generate forcegraph plot of revigo GO graph

In alexvpickering/revigoR: Scrape revigo webapp and plot results

Description

Forcegraph uses nodes and links from cytoscape map file.

Usage

revigo_forcegraph(data_dir)

Arguments

data_dir

Directory to store revigo scripts and output files

Details

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.

Value

r2d3 plot

See Also

add_path_genes to enable heatplots on hover.

Examples

# single analysis
data(go_up2)
data_dir1 <- tempdir()
scrape_revigo(data_dir1, go_up2)
revigo_forcegraph(data_dir1)

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

data_dir2 <- tempdir()
scrape_revigo(data_dir2, go_up)
revigo_forcegraph(data_dir2)

alexvpickering/revigoR documentation built on March 17, 2021, 8:09 p.m.