produce_volcano: produce a volcano plot from DESeq2 results

In CharlesJB/rnaseq: Wrapper Functions for RNA-Seq Post-Processing

produce a volcano plot from DESeq2 results

Description

produce a volcano plot from DESeq2 results

Usage

produce_volcano(
  de_res,
  fc_threshold = 3,
  p_threshold = 0.05,
  y_axis = "padj",
  show_signif_counts = TRUE,
  show_signif_lines = "vertical",
  show_signif_color = TRUE,
  col_up = "#E73426",
  col_down = "#0020F5",
  size = 3,
  graph = TRUE,
  title = NA
)

Arguments

de_res	the data.frame object returned by the DESeq2::results function.
fc_threshold	The threshold of FC to be considered as significant. Default: 0.05
p_threshold	The threshold of p stat to be considered as significant. Default: 1.5
y_axis	Statistical results to show in volcano plot. "pvalue" or "padj". Defauld: "padj"
show_signif_counts	show the number of up- and down-regulated genes?
show_signif_lines	show lines at the threshold for significance? "none", "vertical","horizontal" or "both". Default: "vertical"
show_signif_color	Show color for significant genes? Default: TRUE
col_up	Color of the up-regulated genes. Default: "#E73426"
col_down	Color of the down-regulated genes. Default: "#0020F5"
size	The size of the points. Default: 3.
graph	produce the graph. true or false. default: true.
title	The title of the graph. If NA, no title will be displayed. Default: NA.

Value

produce the volcano plot and silently returns the ggplot object and the data.frame used. # TODO: data.frame w anno, df signif

Examples

txi <- get_demo_txi()
design <- get_demo_design()
dds <- deseq2_analysis(txi, design, ~ group)
de <- DESeq2::results(dds, contrast = c("group", "A", "B"))
volcano <- produce_volcano(de, graph = FALSE)

CharlesJB/rnaseq documentation built on Oct. 17, 2023, 5:37 p.m.