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Plot GO enrichment

Source: R/plot_GO.R
plot_GO.Rd

Visualization of GO enrichment analysis with dotplot, cnetplot, or emapplot in clusterProfiler

Usage

plot_GO(
  go_list,
  plot_dotplot = FALSE,
  plot_cnetplot = FALSE,
  plot_emapplot = FALSE,
  showCategory_dotplot = 5,
  showCategory_cnetplot = 5,
  showCategory_emapplot = 5,
  fontsize = 8,
  label = "features",
  ...
)

Arguments

go_list

A list of enriched GO results, output from enrichGO_list()

plot_dotplot

Whether to plot dotplot (default is TRUE)

plot_cnetplot

Whether to plot cnetplot (default is FALSE)

plot_emapplot

Whether to plot emapplot (default is FALSE)

showCategory_dotplot

showCategory parameter of clusterProfiler::dotplot() (default is 5)

showCategory_cnetplot

showCategory parameter of clusterProfiler::cnetplot() (default is 5)

showCategory_emapplot

showCategory parameter of clusterProfiler::emapplot() (default is 5)

fontsize

Font size for the plots (default is 8)

label

Title for the plots (default is "genes")

...

Additional parameters to pass to the plotting functions clusterProfiler::dotplot(), clusterProfiler::cnetplot(), or clusterProfiler::emapplot()

Value

A series of plots visualizing the GO enrichment results.

Examples

library(dplyr)
library(org.Mm.eg.db)
data(example_net)
example_module <- data.frame(Module = as.factor(example_net$colors)) %>%
    tibble::rownames_to_column("Feature") %>% arrange(Module)
# select two modules for demonstration
example_module_list <- example_module %>% 
    filter(Module %in% c(1, 2)) %>%
    split(as.character(.$Module)) %>%
    lapply(`[[`, "Feature")
# set cutoff to 1 to show all results for demonstration
example_go_list = enrichGO_list(example_module_list, OrgDb = org.Mm.eg.db,
    universe = example_module$Feature,
    pvalueCutoff = 1, qvalueCutoff = 1,
    category = "BP", simplify = FALSE)
#> Performing GO enrichment for category: BP
#> Processing gene list: 1
#> 'select()' returned 1:1 mapping between keys and columns
#> 'select()' returned 1:1 mapping between keys and columns
#> Warning: 1.03% of input gene IDs are fail to map...
#> Processing gene list: 2
#> 'select()' returned 1:1 mapping between keys and columns
#> Warning: 5.88% of input gene IDs are fail to map...
#> 'select()' returned 1:1 mapping between keys and columns
#> Warning: 1.03% of input gene IDs are fail to map...
#> Merging GO enrichment results across gene lists for each category.
plot_GO(example_go_list$all, plot_dotplot = TRUE,
    plot_emapplot = FALSE, plot_cnetplot = FALSE)