olink_boxplot {OlinkAnalyze} | R Documentation |
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)
anova_results <- olink_anova(npx_data1, variable = "Site")
significant_assays <- anova_results %>%
filter(Threshold == 'Significant') %>%
pull(OlinkID)
olink_boxplot(npx_data1,
variable = "Site",
olinkid_list = significant_assays,
verbose = TRUE,
number_of_proteins_per_plot = 3)