Plot Time Series Data for a gene or phospho site from SummarizedExperiment object

plotTimeSeries plots time series data for a given gene or phospho site from a given SummarizedExperiment object, allowing different types of plots such as expression, log fold change, or two-condition expression.

Usage

plotTimeSeries(
  se,
  type = c("expression", "logFC", "two-condition expression"),
  geneID,
  symbol,
  condition,
  treatment,
  refTreat,
  addZero = FALSE,
  zeroTreat = NULL,
  timerange
)

Arguments

se

A SummarizedExperiment object containing the data.

type

Character. The type of plot to generate. Options are " expression", "logFC", or "two-condition expression".

geneID

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.

condition

Character. The condition corresponds to one of the columns from the colData of SE object.

treatment

Character. The treatment to use for filtering the data.

refTreat

Character. The reference treatment to compare against.

addZero

Logical, whether to add a zero time point to the data. Default is FALSE.

zeroTreat

Character. The treatment to use for adding the zero time point. Default is NULL.

timerange

Character vector.The range of time points to include in the plot.

Value

A ggplot2 object representing the time series plot.

Details

This function generates time series plots for a specified gene or feature from a SummarizedExperiment (SE) object. The type of plot can be one of the following: - "expression": Plots normalized expression levels over time. - "logFC": Plots log fold change (logFC) over time, comparing a treatment to a reference treatment. - "two-condition expression": Plots normalized expression levels over time for two conditions.

The function can add a zero time point if specified and handles data with and without subject-specific information. The plot includes points for each time point and a summary line representing the mean value.

The x-axis represents time, and the y-axis represents the selected metric (normalized expression or logFC). The plot is customized with various aesthetic elements, such as point size, line type, 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)
# Plot a specific gene experssion over time
timerange <- unique(se$timepoint)
plotTimeSeries(result, type = "expression", geneID = "p18",
symbol = "TMEM238", condition = "treatment", treatment = "EGF",
timerange = timerange)