In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(RNAseqStat)

GO

Enrichment analysis of GO will be done in this Step.

enrichGO_run(DEG_df, x = "log2FoldChange", y = "pvalue", dir = results_dir)

Resluts Overview

fl <- list.files("../dev/example_output/")
modules <- fl[grep("3-EnrichGO.*.pdf",fl)]
bitmap_l <- lapply(modules, function(x){
  pdftools::pdf_render_page(glue::glue("../dev/example_output/{x}"), page = 1, dpi = 300)
})
basenames <- gsub(pattern = "\\.pdf$", "", modules)
names(bitmap_l) <- basenames
tmp <- lapply(seq_along(bitmap_l), function(x){
  png::writePNG(bitmap_l[[x]], glue::glue("{names(bitmap_l)[[x]]}.png"))
})

knitr::include_graphics("3-EnrichGO_barplot-gene_Up_GO_enrichment.png")

knitr::include_graphics("3-EnrichGO_barplot-gene_Down_GO_enrichment.png")

knitr::include_graphics("3-EnrichGO_barplot-gene_diff_GO_enrichment.png")

xiayh17/RNAseqStat documentation built on June 16, 2022, 11:51 a.m.