plot_volcano: Volcano plot

In vari-bbc/bbcRNA: Bulk RNA-seq workflow for VAI BBC

Description

Plot volcano plots for contrasts in edger or deseq2 slot of BbcSE object

Usage

plot_volcano(
  x,
  de_method = "edger",
  gene_name = "gene_symbol",
  pval_name = "FDR",
  pvalCutoff = 0.05,
  y_title = paste0("-Log10 (", pval_name, ")"),
  contrast_names,
  ...
)

Arguments

x	A BbcSE object
de_method	"edger" or "deseq2"
gene_name	"gene_symbol" or "ensembl_id". Corresponds to columns in 'bbcRNA::get_de_table()' output
pval_name	"PValue" or "FDR". Corresponds to columns in 'bbcRNA::get_de_table()' output
pvalCutoff	"Cut-off for statistical significance. A horizontal line will be drawn at -log10(pCutoff)." See EnhancedVolcano documentation.
y_title	Y axis label
contrast_names	character value or vector for the contrast(s) of interest. See name(de_results(edger(x))). If not specified, then all contrasts will be processed.
...	Passed to EnhancedVolcano::EnhancedVolcano

Value

A list of ggplot objects

See Also

EnhancedVolcano

vari-bbc/bbcRNA documentation built on Nov. 10, 2020, 11:09 p.m.