PlotPCA: PCA plots of data for QC

In Mathelab/IntLIM: Integration of Omics Data Using Linear Modeling

PCA plots of data for QC

Description

PCA plots of data for QC

Usage

PlotPCA(inputData, viewer = T, stype = NULL, common = T,
  palette = "Set1")

Arguments

inputData	IntLimObject output of ReadData()
viewer	whether the plot should be displayed in the RStudio viewer (T) or in Shiny/Knittr (F)
stype	category to color-code by (can be more than two categories)
common	whether or not samples that are in common between the metabolite and gene expression datasets should be plotted (T/F); default is TRUE
palette	choose an RColorBrewer palette ("Set1", "Set2", "Set3", "Pastel1", "Pastel2", "Paired", etc.) or submit a vector of colors

Value

a highcharter object

Examples

dir <- system.file("extdata", package="IntLIM", mustWork=TRUE)
csvfile <- file.path(dir, "NCItestinput.csv")
mydata <- ReadData(csvfile,metabid='id',geneid='id')
PlotPCA(mydata,stype = "PBO_vs_Leukemia")

Mathelab/IntLIM documentation built on July 9, 2022, 5:10 p.m.