PlotPCA: Plot PCA

In flajole/MApckg: R package of MetaboAnalyst functions

Description

Set of functions for plotting the results of PCA.

PlotPCAPairSummary - plot summary.

PlotPCAScree - plot scree plot of varience explained by PC.

PlotPCA2DScore - plot 2D score plot.

PlotPCABiplot - plot the biplot.

PlotPCALoadings - plot loadings.

Usage

PlotPCAPairSummary(dataSet, analSet, imgName = "pca_pair_", format = "png",
  dpi = 72, width = NA, pc.num = 2)

PlotPCAScree(dataSet, analSet, imgName = "pca_scree_", format = "png",
  dpi = 72, width = NA, scree.num)

PlotPCA2DScore(dataSet, analSet, imgName = "pca_score2d_", format = "png",
  dpi = 72, width = NA, inx1 = 1, inx2 = 2, reg = 0.95, show = TRUE,
  gray.scale = FALSE)

PlotPCABiplot(dataSet, analSet, imgName = "pca_biplot_", format = "png",
  dpi = 72, width = NA, inx1 = 1, inx2 = 2)

PlotPCALoadings(dataSet, analSet, imgName = "pca_loading_", format = "png",
  dpi = 72, width = NA, plotType = "scatter", show = TRUE)

Arguments

dataSet	List, data set object generated by MS_to_MA function.
analSet	List, containing the results of statistical analysis (can be just an empty list).
imgName	Image file name prefix.
format	Image format, one of: "png", "tiff", "pdf", "ps", "svg"
dpi	Image resolution.
width	Image width.
pc.num	The number of plotted principal components.
scree.num	The total number of plotted PCs.
inx1, inx2	The order numbers of PCs.
reg	Set the confidence level for plotting confidence region ellipse.
show	If TRUE then points at the plot are labeled.
gray.scale	If TRUE then plot is colored in 50 shades of gray.
plotType	"scatter" for scatter plot or "boxplot" for box plot

See Also

PCA.Anal, PCA.Loadings

flajole/MApckg documentation built on May 16, 2019, 1:16 p.m.