PlotPCA: Plot PCA

Description Usage Arguments See Also

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

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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.