olink_volcano_plot: Easy volcano plot with Olink theme

In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

Easy volcano plot with Olink theme

Description

Generates a volcano plot using the results of the olink_ttest function using ggplot and ggplot2::geom_point. The estimated difference is plotted on the x-axis and the negative 10-log p-value on the y-axis. The horizontal dotted line indicates p-value=0.05. Dots are colored based on the Benjamini-Hochberg adjusted p-value cutoff 0.05 and can optionally be annotated by OlinkID.

Usage

olink_volcano_plot(p.val_tbl, x_lab = "Estimate", olinkid_list = NULL, ...)

Arguments

p.val_tbl	a data frame of results generated by olink_ttest()
x_lab	Optional. Character value to use as the X-axis label
olinkid_list	Optional. Character vector of proteins (by OlinkID) to label in the plot. If not provided, default is to label all significant proteins.
...	Optional. Additional arguments for olink_color_discrete()

Value

An object of class "ggplot", plotting significance (y-axis) by estimated difference between groups (x-axis) for each protein.

Examples

if (rlang::is_installed(pkg = c("broom", "ggrepel"))) {
  npx_df <- npx_data1 |>
  dplyr::filter(
    !grepl(pattern = "control",
           x = .data[["SampleID"]],
           ignore.case = TRUE

     )
  )

  check_log <- check_npx(df = npx_df)

  ttest_results <- OlinkAnalyze::olink_ttest(
    df = npx_df,
    check_log = check_log,
    variable = "Treatment",
    alternative = "two.sided"
  )

  OlinkAnalyze::olink_volcano_plot(
    p.val_tbl = ttest_results
  )
}

OlinkAnalyze documentation built on June 24, 2026, 1:06 a.m.