olink_boxplot: Function which plots boxplots of selected variables

In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

Function which plots boxplots of selected variables

Description

Generates faceted boxplots of NPX vs. grouping variable(s) for a given list of proteins (OlinkIDs) using ggplot and ggplot2::geom_boxplot.

Usage

olink_boxplot(
  df,
  variable,
  olinkid_list,
  verbose = FALSE,
  number_of_proteins_per_plot = 6,
  posthoc_results = NULL,
  ttest_results = NULL,
  ...
)

Arguments

df	NPX data frame in long format with at least protein name (Assay), OlinkID (unique), UniProt and at least one grouping variable.
variable	A character vector or character value indicating which column to use as the x-axis and fill grouping variable. The first or single value is used as x-axis, the second as fill. Further values in a vector are not plotted.
olinkid_list	Character vector indicating which proteins (OlinkIDs) to plot.
verbose	Boolean. If the plots are shown as well as returned in the list (default is false).
number_of_proteins_per_plot	Number of boxplots to include in the facet plot (default 6).
posthoc_results	Data frame from ANOVA posthoc analysis using olink_anova_posthoc() function.
ttest_results	Data frame from ttest analysis using olink_ttest() function.
...	coloroption passed to specify color order

Value

A list of objects of class “ggplot” (the actual ggplot object is entry 1 in the list). Box and whisker plot of NPX (y-axis) by variable (x-axis) for each Assay

Examples

library(dplyr)
npx_df <- npx_data1 |> filter(!grepl('control|ctrl',SampleID, ignore.case = TRUE))
anova_results <- olink_anova(npx_df, variable = "Site")
significant_assays <- anova_results |>
    filter(Threshold == 'Significant') |>
    pull(OlinkID)
olink_boxplot(npx_df,
              variable = "Site",
              olinkid_list = significant_assays,
              verbose = TRUE,
              number_of_proteins_per_plot = 3)

OlinkAnalyze documentation built on April 4, 2025, 3:26 a.m.