OlinkAnalyze (version 4.2.0)

olink_boxplot: 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,
  ...
)

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

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

Examples

# \donttest{

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)# }