go.results.to.latex: LaTeX output for Gene Ontology Enrichment results

In cellTree: Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure

Description

Outputs or writes result tables of Gene Ontology enrichment testing in LaTeX format.

Usage

go.results.to.latex(go.results, tex.file.name = "go_terms.tex",
  topic.colors = rainbow(length(go.results$all)))

Arguments

go.results	GO Enrichment result list object, such as returned by compute.go.enrichment.
tex.file.name	String (optional). If not NULL: name of the file to save to.
topic.colors	RGB colour vector (optional). Colors to use for each topic.

Value

GO enrichment results in LaTeX format

Examples

# Load pre-computed LDA model for skeletal myoblast RNA-Seq data from HSMMSingleCell package:
data(HSMM_lda_model)


# Load GO mapping database for 'homo sapiens':
library(org.Hs.eg.db)
# Compute GO enrichment sets for each topic:
go.results = compute.go.enrichment(HSMM_lda_model, org.Hs.eg.db, bonferroni.correct=TRUE)

# Output LaTeX tables for GO results
latex.table = go.results.to.latex(go.results, tex.file.name='go_results.tex')

# [Optional] compile LaTeX to PDF (need to have LaTeX binaries installed):
library('tools')
texi2pdf('go_results.tex')
library('Biobase')
openPDF('go_results.pdf')

cellTree documentation built on Nov. 8, 2020, 5:05 p.m.