plotPCA: Plot Heatmap

In ELELAB/lipidQ: Lipidomics Analysis Tool

Description

This function plots the following PCA plots: screeplot and biplot

Usage

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

Arguments

data	quantified data to be visualized (finalOutput_molPct.csv)
sampleTypes	file that associates column names of MS1 with sampleTypes
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

four plot images: a scree plots (screePlot_species.png & screePlot_classes.png) and a biplot (PCA_biplot_species.png & PCA_biplot_classes.png) for both species and classes.

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 pca scree and biplot from log2 transformed data with 0.0001 added
# pseudo counts
plotPCA(data, sampleTypes, pathToOutput = "", log2 = TRUE,
 pseudoCount = 0.0001)

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