met.plot_PCAScree: Plot PCA scree plot

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

Plot PCA scree plot

Description

met.plot_PCAScree visualizes the proportion of variance explained for each principal component.

Usage

met.plot_PCAScree(
  mSetObj = NA,
  imgName = "PCA_ScreePlot",
  format = "pdf",
  dpi = NULL,
  width = NA,
  scree.num,
  plot = TRUE,
  export = FALSE
)

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)
width	(Numeric) width of the the image file in inches (if export = TRUE).
scree.num	Numeric, input a number to indicate the number of principal components to display in the scree plot.
plot	(Logical, TRUE or FALSE) Shall the plot be returned in the RStudio 'Plots' pane?
export	(Logical, TRUE or FALSE) Shall the plot be exported as PDF or PNG file?

Value

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

Author(s)

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

References

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

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