plot_string: Plot STRING network of genes colored by enriched pathways

In BIGslu/BIGpicture: Standard Plots for BIGslu

Plot STRING network of genes colored by enriched pathways

Description

To be used in conjunction with map_string

Usage

plot_string(
  map,
  layout = "fr",
  edge_min = 0,
  edge_max = Inf,
  enriched_only = FALSE,
  enrichment = NULL,
  overlap = 2,
  fdr_cutoff = 0.2,
  colors = NULL,
  text_size = 2,
  node_size = 1
)

Arguments

map	List output by map_string
layout	Character string for network layout algorithm. See options in igraph::layout_with_
edge_min	Numeric minimum edges a node must have to be displayed. Default is 0 meaning orphan nodes are included
edge_max	Numeric maximum edges a node must have to be displayed. Default in Inf. Set to 0 to see only orphan nodes
enriched_only	Logical if should include only genes in significantly enriched terms. Default FALSE
enrichment	Data frame output by BIGprofiler, BIGenrichr, or BIGsea. For use in coloring nodes
overlap	Numeric minimum of total significant genes in a enrichment term to be used as colors (BIGprofiler, BIGenrichr)
fdr_cutoff	Numeric maximum FDR of enrichment terms to be used as colors (BIGprofiler, BIGenrichr, BIGsea)
colors	Character vector of custom colors to use. Must be at least a long as total significant terms plus 1 for the "none" group
text_size	Numeric size of gene labels on network nodes. Default of 2
node_size	Numeric size of network nodes. Default of 1

Value

ggplot STRING network object

Examples

#NOT RUN
# map <- map_string(genes = c("MTHFD2","ISOC1","IL2RB","SAMHD1","NAMPT","NOD1",
#                            "NFKB1","IFIT3","ZBP1","IL15RA","SP110","ITGB7",
#                            "SERPING1","B2M","CXCL11","USP18","MAPKAPK2","DKK1"),
#                version = 12, score_threshold = 400)
# plot_string(map)
#
# Add enrichment colors
# library(dplyr)
# library(SEARchways)
# genes.OI <- example.model$lmerel %>%
#             filter(variable == "virus" & FDR < 0.2) %>%
#             select(variable, gene)
# example_enrich <- SEARchways::BIGprofiler(gene_df = genes.OI,
#                                           category = "H", ID = "ENSEMBL")
#
# map2 <- map_string(genes = genes.OI$gene,
#                  version = 11.5, score_threshold = 400)
# plot_string(map2, enrichment = example_enrich, fdr_cutoff=0.2)
# plot_string(map2, enrichment = example_enrich, fdr_cutoff=0.2, enriched_only=TRUE)
#
# Add GSEA colors
# genes.FC <- example.model$lmerel %>%
#             filter(variable == "virus") %>%
#             select(variable, gene, estimate)
# example_gsea <- BIGsea(gene_df = genes.FC, category = "H", ID = "ENSEMBL")
#
# plot_string(map2, enrichment = example_gsea, fdr_cutoff = 0.3,
#             edge_max = 0, enriched_only=TRUE)

BIGslu/BIGpicture documentation built on Oct. 14, 2024, 9:30 p.m.