panyq357/onto-scripts

Some scripts to prepare ontology long table for enrichment and GSEA analysis.

Requirements

python3 -m pip install pandas owlready2 retrying openpyxl

Fetch ontologies from Oryzabase

• Oryzabase annotation

python3 scripts/get_ontologies_from_oryzabase.py

Clean JGI Sitalica annotation info

• JGI Sitalica annotation

python3 scripts/clean_jgi_si_annotation.py

Enrichment Analysis using clusterProfiler

install.packages("readxl")
install.packages("BiocManager")
BiocManager::install("clusterProfiler")

onto = readxl::read_excel("results/oryzabase-ontologies.xlsx", sheet="RAP_GO")

gene = c("Os01g0118100", "Os01g0549700", "Os02g0710800", "Os03g0108600", "Os03g0158200", "Os03g0746500")
universe = NULL

enrich_res = clusterProfiler::enricher(
    gene=gene,
    universe=universe,
    TERM2GENE=onto[c("OntoID", "GeneID")],
    TERM2NAME=onto[c("OntoID", "Description")]
)

write.csv(as.data.frame(enrich_res), "enrich_res.csv")

svg("demo_dotplot.svg")
clusterProfiler::dotplot(enrich_res)
dev.off()