volcanoPlot: Volcano Plot Generator To Summarize Univariate Protein...

In pranavdorbala/proteomicsHF: ARIC Proteomics of Heart Failure -- Biomarker Discovery Pipeline

Description

This function takes in plot data and uses it to construct a Volcano Plot to visualize significance. The legend is dependent on the derivation and validation sets. As currently implemented, this function must have both datasets bound.

Usage

volcanoPlot(data, .pval1, .pval2, suffix, ...)

Arguments

data	The plot data (with vars hazr and pval) to create volcano plot with.
.pval1	The significance indicator for scaling 0.05 for the derivation dataset. The number of comparisons must be provided (i.e. 4877 for bonferroni or 1 for FDR).
.pval2	The significance indicator for scaling 0.05 for the validation dataset. The number of comparisons must be provided (i.e. 4877 for bonferroni or 1 for FDR).
suffix	The Suffix that is used on the data join to separate the Derivation and Validation Sets.
...	Additional Parameters (such as title) to be passed to EnhancedVolcano::EnhancedVolcano()

Value

A Volcano Plot, comparing Hazard Ratio against -log10(pvalue)

Examples

## Not run: 

plot.data.visit.five <-
  dplyr::left_join(univariate.results,
                   validation.results,
                   by = "term",
                   suffix = c(".V5", ".V3"))

  volcanoPlot(plot.data.visit.five,
              length(proteins),
              length(bonferroni$kept),
              suffix = c(".V5", ".V3"))


## End(Not run)

pranavdorbala/proteomicsHF documentation built on March 9, 2021, 12:22 a.m.