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

library(dplyr)

npx_df <- npx_data1 %>% filter(!grepl('control',SampleID, ignore.case = TRUE))
ttest_results <- olink_ttest(df=npx_df,
                             variable = 'Treatment',
                             alternative = 'two.sided')
olink_volcano_plot(ttest_results)

OlinkAnalyze documentation built on Nov. 4, 2023, 1:07 a.m.