doSummaryPlot: Wrapper function to generate PCA plot and RSD statistics plot

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

Description

Wrapper function to generate PCA plot and RSD statistics plot

Usage

doSummaryPlot(
  Data,
  classes,
  plotTitle = "PCA",
  blank = "BLANK",
  PQN = FALSE,
  mv_impute = TRUE,
  glogScaling = TRUE,
  scale = TRUE,
  qc_label = "QC",
  ignorelabel = "Removed",
  output = "PCA_plot.pdf",
  labels = "QC",
  qc_shape = 17L,
  base_size = 10L,
  pccomp = c(1L, 2L),
  plot = TRUE
)

Arguments

Data	Data frame.
classes	Vector of class labels.
plotTitle	Title to use for plot output
blank	Label used for blank samples, if set to NULL no samples will be removed
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
qc_label	Label used for QC samples. If set to NULL, assumes that no QC samples are present in data set
ignorelabel	Label for samples which should be excluded from processed data
output	File name for pdf output
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_shape	Shape symbol to use for QC samples
base_size	Ggplot font size
pccomp	PCA components to plot
plot	If set to T will output pdf file, otherwise ggplot object

Value

Summary plot as ggplot object or directly to the pdf file.

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