Network of cosine similarity between terms

Links showing cosine similarity between terms, calculated by topic~term probability matrix or GSEA result. Node pie shows topic distribution of each term or enrichment score distribution of each term.

cosine_network_term(
  SeuratObj,
  cosine_cal_by = "Topic modeling",
  pie_by = "Topic modeling",
  GSEA_by = "GO",
  topn = 10,
  layout = "fr",
  cos_sim_thresh = 0.8,
  SEED = 123,
  radius = 0.1,
  width_range = c(0.05, 0.55),
  text_size = 2
)

Arguments

SeuratObj	Object of class "Seurat"
cosine_cal_by	calculate cosine similarity by topic~term probability matrix or GSEA result. "Topic modeling", "GSEA result".
pie_by	what node pie shows. topic distribution or enrichment score distribution of each term. "Topic modeling", "GSEA result".
GSEA_by	using which GSEA result to run topic modeling, one of "GO", "KEGG", "Reactome", "MSigDb", "WikiPathways", "DO", "NCG", "DGN"
topn	top n terms of each topic or each cluster
layout	network layout
cos_sim_thresh	only shows edge of cosine similarity greater than specific threshold
SEED	seed
radius	node pie radius
width_range	range of width of edges
text_size	size of node labels

Value

ggplot object

Examples

if (FALSE) {
cosine_network_term(SeuratObj, cosine_cal_by = "Topic modeling", pie_by = "Topic modeling",
                    GSEA_by = "GO", topn = 10, layout = "fr", cos_sim_thresh = 0.8,
                    radius = 0.1, text_size = 2)
cosine_network_term(SeuratObj, cosine_cal_by = "GSEA result",
                    pie_by = "GSEA result", GSEA_by = "GO")
# edge(cosine similarity calculation) and node pie information could be different.
cosine_network_term(SeuratObj, cosine_cal_by = "GSEA result",
                    pie_by = "Topic modeling", GSEA_by = "GO")
}