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Plot Heatmap of Intensity assay

Source: R/basic_visualizations.R
plotHeatmap.Rd

plotHeatmap generates a heatmap for intensity assay for different conditions, including top variants, differentially expressed genes, and selected time series clusters.

Usage

plotHeatmap(
  type = c("Top variant", "Differentially expressed", "Selected time series cluster"),
  se,
  data = NULL,
  top = 100,
  cutCol = 1,
  cutRow = 1,
  clustCol = TRUE,
  clustRow = TRUE,
  annotationCol = NULL,
  title = NULL
)

Arguments

type

A character string specifying the type of heatmap to plot. Options are "Top variant", "Differentially expressed", and "Selected time series cluster".

se

A SummarizedExperiment object containing the imputed intensity assay.

data

An optional data frame containing additional data for "Differentially expressed" and "Selected time series cluster" types. Default is NULL.

top

A numeric value specifying the number of top variants to plot. Default is 100.

cutCol

A numeric value specifying the number of clusters for columns. Default is 1.

cutRow

A numeric value specifying the number of clusters for rows. Default is 1.

clustCol

A logical value indicating whether to cluster columns. Default is TRUE.

clustRow

A logical value indicating whether to cluster rows. Default is TRUE.

annotationCol

A character vector specifying the columns in the metadata to use for annotation. Default is NULL.

title

A character string specifying the title of the heatmap. Default is NULL.

Value

A pheatmap object showing the heatmap of Intensity data.

Details

This function creates a heatmap using the Intensity assay from a SummarizedExperiment object. The heatmap can show the top variants based on standard deviation, differentially expressed genes, or selected time series clusters. Row normalization is performed, and the heatmap can include annotations based on specified metadata columns.

Examples

library(SummarizedExperiment)
# Load multiAssayExperiment object
data("dia_example")
# Get SummarizedExperiment object
se <- dia_example[["Phosphoproteome"]]
colData(se) <- colData(dia_example)
# Generate the imputed assay
result <- preprocessPhos(seData = se, normalize = TRUE, impute = "QRILC")
#> Imputing along margin 2 (samples/columns).
# Plot heatmap for top variant
plotHeatmap(type = "Top variant", top = 10, se = result, cutCol = 2)