plotHeatmap: Plot Heatmap

In ELELAB/lipidQ: Lipidomics Analysis Tool

Description

This function plots heatmaps of the data

Usage

plotHeatmap(data, sampleTypes, k = NULL, pathToOutput = "", log2 = FALSE,
  pseudoCount = NULL)

Arguments

data	quantified data to be visualized (finalOutput_molPct.csv)
sampleTypes	file that associates column names of MS1 with the sample types
k	number of k in the k-means algorithm.
pathToOutput	the directory path to save the plots
log2	logical argument that specifies whether or not data has to be log2 transformed
pseudoCount	pseudo count added to the data if the data is log2 transformed in order to avoid negative infinite values in the data

Value

Two heatmap images: heatmap of species (heatmapSpecies_k_n.png) and heatmap of classes (heatmapClasses_k_n.png), where n indicates the amount of clusters k. If clusters are not chosen by the user, a majority vote chart will also be included called nbclustResults.png.

Author(s)

André Vidas Olsen

Examples

# load sample types file and data to be used for visualization
sampleTypes <- read.csv(system.file("extdata", "sampleTypes.csv",
 package = "lipidQ"), stringsAsFactors = FALSE)

data <- read.csv(system.file("extdata/dataTables/checks",
 "finalOutput_molPct.csv", package = "lipidQ"), stringsAsFactors = FALSE)


# create heatmap from log2 transformed data with 0.0001 added pseudo counts
plotHeatmap(data = data, sampleTypes = sampleTypes, k = 2,
 pathToOutput = "",
 log2 = TRUE, pseudoCount = 0.0001)

ELELAB/lipidQ documentation built on Feb. 24, 2020, 12:54 a.m.