hierarchicalPlot: Hierarchical clustering plot

In crukci-bioinformatics/qPLEXanalyzer: Tools for quantitative proteomics data analysis

Hierarchical clustering plot

Description

Computes and displays hierarchical clustering plot for samples in MSnSet

Usage

hierarchicalPlot(
  MSnSetObj,
  sampleColours = NULL,
  colourBy = "SampleGroup",
  horizontal = TRUE,
  title = ""
)

Arguments

MSnSetObj	MSnSet; an object of class MSnSet
sampleColours	character: a named vector of colors for samples, names should be values of colourBy column
colourBy	character: column name from pData(MSnSetObj) to use for coloring samples
horizontal	logical: define orientation of the dendrogram
title	character: the main title for the dendrogram

Value

An object created by ggplot

Examples

data(exp3_OHT_ESR1)
MSnSet_data <- convertToMSnset(exp3_OHT_ESR1$intensities_qPLEX1, 
                               metadata=exp3_OHT_ESR1$metadata_qPLEX1,
                               indExpData=c(7:16), 
                               Sequences=2, 
                               Accessions=6)
exprs(MSnSet_data) <- exprs(MSnSet_data)+0.01
hierarchicalPlot(MSnSet_data, title="qPLEX_RIME_ER")

crukci-bioinformatics/qPLEXanalyzer documentation built on Sept. 24, 2024, 1:13 a.m.