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Meta-analysis volcano plot

Source: R/07_visualize.R
mx_volcano.Rd

Creates a volcano plot from a metaXpressResult object, displaying meta-analysis effect sizes (log2 fold-change) against statistical significance (-log10 meta_padj). The top differentially expressed genes are labelled. Volcano plots are a standard visualization for differential expression results (Li 2012).

Usage

mx_volcano(
  meta_result,
  padj_threshold = 0.05,
  lfc_threshold = 1,
  label_top = 10,
  title = NULL
)

Arguments

meta_result

A metaXpressResult object.

padj_threshold

Numeric. Adjusted p-value threshold for colouring significant genes. Default: 0.05.

lfc_threshold

Numeric. Log2 fold-change threshold. Default: 1.

label_top

Integer. Number of top significant genes to label. Default: 10.

title

Character scalar. Plot title. Default: NULL (auto).

Value

A ggplot2 object.

References

Li, W. (2012) Volcano plots in analyzing differential expressions with mRNA microarrays. Journal of Bioinformatics and Computational Biology, 10(6), 1231003. doi:10.1142/S0219720012310038

See also

mx_forest, mx_heatmap

Examples

if (FALSE) { # \dontrun{
  p <- mx_volcano(meta_result)
  print(p)
} # }