olink_volcano: Volcano plot of Olink results

In ge11232002/OlinkR: A toolkit for Olink data analysis

Description

Given the tibble object from olink_limma, plot a volcano plot. The log2FC is on the x-axis and -log10(P.value) is on y-axis. By default, significant proteins are labeled on the volcano plot.

Usage

olink_volcano(tb, p.value = 0.05, log2FC = 0, olinkIds = NULL)

Arguments

tb	A tibble object from olink_limma function.
p.value	numeric(1): The p.value cutoff for significance level.
log2FC	numeric(1): The log2FC cutoff for significance level.
olinkIds	character(n): OlinkIDs to label on the volcano plot.

Value

A ggplot object.

Author(s)

Ge Tan

Examples

npxFn <- system.file("extdata",
                     c("20200507_Inflammation_NPX_1.xlsx",
                       "20200625_Inflammation_NPX_2.xlsx"),
                     package = "OlinkR")
metaFn <- system.file("extdata", "Inflammation_Metadata.xlsx",
                      package = "OlinkR")
se <- as_se(read_npx(npxFn, metaFn))
tb <- olink_limma(se,
  factorCol = "condition_Factor",
  contrasts = "Glucose.10mM.Vehicle - Vehicle.Vehicle",
  blocking = "Donor_Factor"
)
olink_volcano(tb)

ge11232002/OlinkR documentation built on Jan. 17, 2022, 8:28 p.m.