Plot Boxplot of Intensity Data

intensityBoxPlot creates a boxplot for the Intensity data of a given gene or feature, with optional subject-specific lines.

Usage

intensityBoxPlot(se, id, symbol)

Arguments

se

A SummarizedExperiment object containing the data.

id

Character. The identifier of the gene or feature to plot.

symbol

Character. The symbol or name of the gene or feature to use as the plot title.

Value

A ggplot2 object representing the boxplot of the intensity data.

Details

This function generates a boxplot for the intensity data of a specified gene or feature from a SummarizedExperiment (SE) object. The plot shows the distribution of normalized intensities across different groups specified in the comparison column of the SE object.

The function can handle both grouped data and repeated measures: - If the SE object does not contain a subjectID column, the function plots a standard boxplot grouped by the comparison column. - If the SE object contains a subjectID column, the function adds lines connecting the points for each subject across the groups, providing a visual indication of subject-specific changes.

The boxplot is customized with various aesthetic elements, such as box width, transparency, point size, axis labels, and title formatting.

Examples

library(SummarizedExperiment)
# Load multiAssayExperiment object
data("dda_example")
# Get SummarizedExperiment object
se <- dda_example[["Proteome"]]
colData(se) <- colData(dda_example)
# Preprocess the proteome assay
result <- preprocessProteome(se, normalize = TRUE)
# Call the function to perform differential expression analyis
de <- performDifferentialExp(se = result, assay = "Intensity",
method = "limma", reference = "1stCrtl", target = "EGF",
condition = "treatment")
# Plot the box plot for the given id and symbol
intensityBoxPlot(de$seSub, "p99", "PPP6C")