Plots GSEA data as volcano plot
Usage
plot_gsea_volcano(
gsea,
padj_cutoff = 0.05,
label = "sig",
top_n = NULL,
up_color = "red3",
down_color = "dodgerblue",
ns_color = "grey70"
)Arguments
- gsea
gsea Output from perform_GSEA.
- padj_cutoff
padj_cutoff The maximum p.adjust value allowed for inclusion of the pathway.
- label
Specifies which points to label. The default is 'sig', labeling all significant points. Entering a value for top_n limits the labeling to the top_n up- and top_n down-regulated proteins based on the p.adj. When providing a vector with protein names, only those points are labeled.
- top_n
Specifies how many significant points to label.
- up_color
Character string specifying the color for significant points with positive NES.
- down_color
Character string specifying the color for significant points with positive NES.
- ns_color
Character string specifying the color for non-significant points.
Examples
if (FALSE) { # \dontrun{
gsea <- perform_GSEA(res, genesets)
volcano <- plot_gsea_volcano(gsea, top_n = 10)
} # }