met.plot_PCA2DLoading: Plot PCA loadings and also set up the matrix for display

In NicWir/VisomX: User-Friendly and Comprehensive Analysis and Visualization of Omics Data

Plot PCA loadings and also set up the matrix for display

Description

met.plot_PCA2DLoading visualizes which features are responsible for the patterns seen among the samples in principal component analysis.

Usage

met.plot_PCA2DLoading(
  mSetObj = NA,
  imgName = "PCA_2DLoadings",
  format = "pdf",
  dpi = NULL,
  subtitle = FALSE,
  width = NA,
  inx1,
  inx2,
  export = TRUE,
  plot = TRUE
)

Arguments

mSetObj	Input name of the created mSet object, Data container after principal component analysis (met.PCA.Anal).
imgName	(Character) Enter a name for the image file (if export = TRUE).
format	(Character, "png" or "pdf") image file format (if export = TRUE).
dpi	(Numeric) resolution of the image file (if export = TRUE). If NULL, the resolution will be chosen automatically based on the chosen file format (300 dpi for PNG, 72 dpi for PDF)
subtitle	(Logical, TRUE or FALSE) Shall the applied data transformation and scaling methods be displayed below the plot title?
width	(Numeric) width of the the image file in inches (if export = TRUE).
inx1	Numeric, indicate the number of the principal component for the x-axis of the loading plot.
inx2	Numeric, indicate the number of the principal component for the y-axis of the loading plot.
export	(Logical, TRUE or FALSE) Shall the plot be exported as PDF or PNG file?
plot	(Logical, TRUE or FALSE) Shall the plot be returned in the RStudio 'Plots' pane?

Value

The input mSet object with added scatter plot. The plot can be retrieved from within R via print(mSetObj$imgSet$pca.loading_PCx_PCy.plot).

Author(s)

Nicolas T. Wirth [e-mail] Technical University of Denmark License: GNU GPL (>= 2)

References

adapted from PlotPCALoading (https://github.com/xia-lab/MetaboAnalystR).

NicWir/VisomX documentation built on Dec. 8, 2024, 1:27 a.m.