olink_lmer_plot: Function which performs a point-range plot per protein on a...

In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

Function which performs a point-range plot per protein on a linear mixed model

Description

Generates a point-range plot faceted by Assay using ggplot and ggplot2::geom_pointrange based on a linear mixed effects model using lmerTest:lmer and emmeans::emmeans. See olink_lmer for details of input notation.

Usage

olink_lmer_plot(
  df,
  check_log = NULL,
  variable,
  outcome = "NPX",
  random,
  olinkid_list = NULL,
  covariates = NULL,
  x_axis_variable,
  col_variable = NULL,
  number_of_proteins_per_plot = 6L,
  verbose = FALSE,
  ...
)

Arguments

df	NPX data frame in long format with at least protein name (Assay), OlinkID, UniProt, 1-2 variables with at least 2 levels.
check_log	A named list returned by check_npx(). If NULL, check_npx() will be run internally using df.
variable	Single character value or character array. Variable(s) to test. If length > 1, the included variable names will be used in crossed analyses. Also takes ':' or '*' notation.
outcome	Character. The dependent variable. Default: NPX.
random	Single character value or character array.
olinkid_list	Character vector indicating which proteins (by OlinkID) for which to create figures.
covariates	Single character value or character array. Default: NULL. Covariates to include. Takes ':' or '*' notation. Crossed analysis will not be inferred from main effects.
x_axis_variable	Character. Which main effect to use as x-axis in the plot.
col_variable	Character. If provided, the interaction effect col_variable:x_axis_variable will be plotted with x_axis_variable on the x-axis and col_variable as color.
number_of_proteins_per_plot	Number plots to include in the list of point-range plots. Defaults to 6 plots per figure
verbose	Boolean. Default: True. If information about removed samples, factor conversion and final model formula is to be printed to the console.
...	coloroption for color ordering

Value

A list of objects of class "ggplot" showing point-range plot of NPX (y-axis) over x_axis_variable for each assay (facet), colored by col_variable if provided.

Examples

if (rlang::is_installed(pkg = c("lme4", "lmerTest", "broom", "emmeans"))) {
  #data
  npx_df <- OlinkAnalyze::npx_data1 |>
    dplyr::filter(
      !grepl(
        pattern = "control|ctrl",
        x = .data[["SampleID"]],
        ignore.case = TRUE
      )
    )

  # check data
  npx_df_check_log <- OlinkAnalyze::check_npx(
    df = npx_df
  )

  # Results in model NPX ~ Time * Treatment + (1 | Subject) + (1 | Site)
  lmer_results <- OlinkAnalyze::olink_lmer(
    df = npx_df,
    check_log = npx_df_check_log,
    variable = c("Time", "Treatment"),
    random = c("Subject")
  )

  # List of significant proteins for the interaction effect Time:Treatment
  assay_list <- lmer_results |>
    dplyr::filter(
    .data[["Threshold"]] == "Significant"
    & .data[["term"]] == "Time:Treatment"
  ) |>
    dplyr::distinct(.data[["OlinkID"]]) |>
    dplyr::pull()

  lst_pointrange_plots <- OlinkAnalyze::olink_lmer_plot(
    df = npx_df,
    check_log = npx_df_check_log,
    variable = c("Time", "Treatment"),
    random = c("Subject"),
    x_axis_variable = "Time",
    col_variable = "Treatment",
    verbose = TRUE,
    olinkid_list = assay_list,
    number_of_proteins_per_plot = 10L
  )
}

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