pca2DPlot: Scatter plot of first 2 principal components

In iCheck: QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data

Description

Scatter plot of first 2 principal components.

Usage

pca2DPlot(pcaObj, 
          plot.dim = c(1,2),
          labelVariable = "subjID", 
          hybName = "Hybridization_Name",
          outFileName = "test_pca_raw.pdf", 
          title = "Scatter plot of pcas", 
          plotOutPutFlag = FALSE, 
          mar = c(5, 4, 4, 2) + 0.1, 
          lwd = 1.5, 
          equalRange = TRUE, 
          xlab = NULL, 
          ylab = NULL, 
          xlim = NULL, 
          ylim = NULL, 
          cex.legend = 1.5, 
          cex = 1.5, 
          cex.lab = 1.5, 
          cex.axis = 1.5, 
          legendPosition = "topright", 
          ...)

Arguments

pcaObj	An object returned by the function pca of the R package pcaMethods.
plot.dim	A vector of 2 positive-integer-value integer specifying which 2 pcas will be plot.
labelVariable	The name of a column of the phenotype data matrix. The elements of the column will replace the column names of the expression data matrix.
hybName	character string. indicating the phenotype variable Hybridization_Name.
outFileName	Name of the figure file to be created.
title	Title of the scatter plot.
plotOutPutFlag	logical. plotOutPutFlag=TRUE indicates the plots will be output to pdf format files. Otherwise, the plots will not be output to external files.
mar	A numerical vector of the form 'c(bottom, left, top, right)' which gives the number of lines of margin to be specified on the four sides of the plot. The default is 'c(5, 4, 4, 2) + 0.1'. see par.
lwd	The line width, a _positive_ number, defaulting to '1'. see par.
equalRange	logical. Indicating if the x-axis and y-axis have the same range.
xlab	Label of x axis.
ylab	Label of y axis.
xlim	Range of x axis.
ylim	Range of y axis.
cex.legend	Font size for legend.
cex	numerical value giving the amount by which plotting text and symbols should be magnified relative to the default. see par.
cex.lab	The magnification to be used for x and y labels relative to the current setting of cex.
cex.axis	The magnification to be used for axis annotation relative to the current setting of cex. see par.
legendPosition	Position of legend. Possible values are “bottomright”, “bottom”, “bottomleft”, “left”, “topleft”, “top”, “topright”, “right” and “center”.
...	Arguments to be passed to plot.

Value

A matrix of PCA scores. Each column corresponds to a principal component.

Author(s)

Weiliang Qiu <[e-mail]>, Brandon Guo <[e-mail]>, Christopher Anderson <[e-mail]>, Barbara Klanderman <[e-mail]>, Vincent Carey <[e-mail]>, Benjamin Raby <[e-mail]>

Examples

    # generate simulated data set from conditional normal distribution
    set.seed(1234567)
    es.sim = genSimData.BayesNormal(nCpGs = 100, 
      nCases = 20, nControls = 20,
      mu.n = -2, mu.c = 2,
      d0 = 20, s02 = 0.64, s02.c = 1.5, testPara = "var",
      outlierFlag = FALSE, 
      eps = 1.0e-3, applier = lapply) 
    print(es.sim)

    pca.obj = getPCAFunc(es = es.sim, 
                     labelVariable = "subjID", 
                     hybName = "memSubj",
                     requireLog2 = FALSE,
                     corFlag = FALSE
)

pca2DPlot(pcaObj = pca.obj, 
          plot.dim = c(1,2),
          labelVariable = "subjID", 
          hybName = "memSubj",
          plotOutPutFlag = FALSE, 
          cex.legend = 0.5, 
          legendPosition = "topright") 
    

iCheck documentation built on Nov. 8, 2020, 11:09 p.m.