Network showing cosine similarity between clusters according to GSEA result

Cosine_networkByGSEA(
  SeuratObj,
  by = "GO",
  layout = layout_nicely,
  cos_sim_thresh = 0.6,
  p.adjust_thresh = 0.05,
  SEED = 123,
  node.cex = 5,
  width_range = c(0.8, 4),
  text_size = 1,
  vertex.label.dist = 0.5
)

Arguments

SeuratObj	Seurat object
by	GO KEGG Reactome MSigDb WikiPathways DO NCG DGN.
layout	layout_nicely, layout_with_fr, etc. Either a function or a numeric matrix. It specifies how the vertices will be placed on the plot.
cos_sim_thresh	only draw links of cosine similarity bigger than this
p.adjust_thresh	threshold of p.adjust to filter pathways used to calculate cosine similarity
SEED	seed
node.cex	node size
width_range	range of width of links
text_size	size of text
vertex.label.dist	The distance of the label from the center of the vertex.

Examples

if (FALSE) {
Cosine_networkByGSEA(SeuratObj, layout=layout_nicely, cos_sim_thresh=0.6,
                     p.adjust_thresh=0.05, SEED=123, node.cex=3, width_range=c(0.1, 0.8))
Cosine_networkByGSEA(SeuratObj, layout=layout_with_fr, cos_sim_thresh=0.8,
                     p.adjust_thresh=0.05, SEED=123, node.cex=5, width_range=c(0.8, 4))
}