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Getting started with some utils functions

emmaplot function

For Network visualisation of fgsea results using emmaplot function

library(data.table)
source('emmaplot.R')

First, load some fgsea results

res_fgsea<-fread('examples_data/res_fgsea_apoe22_vs_33_microglia.csv.gz')

This data.table should have at least the columns pathway, NES and leadingEdge.

filter it to show only the pathways that you want to display. For example the top80 enriched based on pvalue

res_fgsea_top<-head(res_fgsea[order(pval)],80)

Plot these pathways with emmaplot

emmaplot(res_fgsea_top)

you can reduce the pathway label size

emmaplot(res_fgsea_top,label.size = 2)

display more diverse pathways

to display more variety of pathways (coming from different source),the results can be prefiltered for top pathways by pathways source (subcategory)

res_gsea_topbycat<-res_fgsea_top[padj<0.05, #select only pathways those with padj<0.05
                                 .SD[head(order(padj),30)], #filter the data.table by source subcategory by keeping only the top30 by subcat
                                 by='subcat']
emmaplot(head(res_gsea_topbycat[order(pval)],80), #subset the top80 pathways according to the pval of the enrichment
         label.size = 2)

this is a ggplot format so the plot can be saved using

ggsave('examples_data/emmaplot_top80_fgsea_apoe22_vs_33_microglia.pdf')

You can see it in examples_data folder. here is how it look like: emmaplot

Filter pathways by a certain gene

You can decided to display only the pathway of a certain gene (i.e this gene is in the leading edge genes of the pathway)

emmaplot(res_fgsea_top,show_pathway_of = 'CDK2')

Get Only the pathways links

For other purpose, you extract the pathways links by using the GetPathwaysLinks function

pathways_links<-GetPathwaysLinks(res_fgsea_top)
pathways_links
pathway1 pathway2
1: GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_REGULATORY_REGION_SEQUENCE_SPECIFIC_DNA_BINDING GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY
2: GOCC_MITOCHONDRION GOBP_SMALL_MOLECULE_METABOLIC_PROCESS
3: REACTOME_RESPONSE_OF_EIF2AK4_GCN2_TO_AMINO_ACID_DEFICIENCY REACTOME_EUKARYOTIC_TRANSLATION_ELONGATION
4: REACTOME_RESPONSE_OF_EIF2AK4_GCN2_TO_AMINO_ACID_DEFICIENCY WP_CYTOPLASMIC_RIBOSOMAL_PROTEINS