Plot Intensity Boxplots

plotIntensity generates boxplots of assay intensities for each sample in a SummarizedExperiment object. Optionally, the boxplots can be colored based on a specified metadata column. The function handles missing values by filtering them out before plotting.

Usage

plotIntensity(se, colorByCol = "none")

Arguments

se

A SummarizedExperiment object containing the assay data and metadata.

colorByCol

A character string specifying the metadata column to use for coloring the boxplots. Default is "none".

Value

A ggplot2 object showing boxplots of intensities for each sample.

Examples

library(SummarizedExperiment)
# Load multiAssayExperiment object
data("dia_example")
# Get SummarizedExperiment object
se <- dia_example[["Phosphoproteome"]]
colData(se) <- colData(dia_example)
# Preprocess the phosphoproteome assay
result <- preprocessPhos(seData = se, normalize = TRUE, impute = "QRILC")
#> Imputing along margin 2 (samples/columns).
# Call the plotting function
plotIntensity(result, colorByCol = "replicate")