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Create an UpSet Plot from SummarizedExperiment Data

Source: R/GetOverview.R
plot_upset.Rd

This function generates an UpSet plot from a given SummarizedExperiment object. It allows for the visualization of overlaps between sets defined by a specific column in the metadata. The function supports subsetting to reference samples and customizable color mapping.

Usage

plot_upset(
  se,
  color_by = NULL,
  label_by = NULL,
  mb.ratio = c(0.7, 0.3),
  only_refs = FALSE
)

Arguments

se

SummarizedExperiment containing all necessary information of the proteomics data set

color_by

String specifying the column to color the samples (If NULL, the condition column of the SummarizedExperiment object is used.)

label_by

String specifying the column in the metadata used to label the samples for the UpSet plot

mb.ratio

A numeric vector of length 2, specifying the barplot and matrix area ratios

only_refs

Logical, if TRUE, only reference samples (ComRef) are included in the plot

Value

ggplot object

Examples

data(tuberculosis_TMT_se)
plot_upset(tuberculosis_TMT_se, color_by = NULL, label_by = NULL,
           mb.ratio = c(0.7, 0.3), only_refs = FALSE)
#> Condition of SummarizedExperiment used!
#> Label of SummarizedExperiment used!