doPCA: Perform PCA analysis ot single data set or list of data sets

In computational-metabolomics/qcrms: Creates quality control output from XCMS output

Description

Perform PCA analysis ot single data set or list of data sets

Usage

doPCA(
  Data,
  classes,
  plotTitle = "PCA",
  PQN,
  mv_impute,
  glogScaling,
  scale = FALSE,
  labels = "QC",
  qc_label,
  qc_shape = 17L,
  base_size = 12L,
  pccomp = c(1L, 2L),
  subtitle = NULL,
  loadings = FALSE,
  loadingsCol = NULL
)

Arguments

Data	Data frame.
classes	Vector of class labels.
plotTitle	Character value to display as the plot title
PQN	Can be set to T or F, to perform PQN normalisation
mv_impute	T or F, indicates if missing value imputation has to be carried
glogScaling	T or F, applie glog transformation to the given data
scale	Perform UV scaling on data
labels	Can be set to "QC" to label only QC samples. "none" to no include labels. If set to any other value will use column names of Data.
qc_label	Label used for QC samples. If set to NULL, assumes that no QC samples are present in data set
qc_shape	Shape symbol to use for QC samples
base_size	Font size for plot fonts
pccomp	PCA components to plot
subtitle	Subtitle to include in PCA plot
loadings	T or F, to include PCA loadings plot or not
loadingsCol	Colors to use for loadings plot

Value

Ggplot object with plot(s)

computational-metabolomics/qcrms documentation built on Jan. 18, 2021, 1:46 a.m.