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Create 2D PCA score plot

Source: R/metabolomics_plots.R
met.plot_PCA2DScore.Rd

met.plot_PCA2DScore visualizes clusters of samples based on their similarity in principal component analysis.

Usage

met.plot_PCA2DScore(
  mSetObj = NA,
  imgName = "PCA_2DScores",
  format = "pdf",
  dpi = NULL,
  subtitle = FALSE,
  width = NA,
  pcx,
  pcy,
  reg = 0.95,
  show = 1,
  grey.scale = 0,
  plot = TRUE,
  export = 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).

pcx

Specify the principal component on the x-axis

pcy

Specify the principal component on the y-axis

reg

Numeric, input a number between 0 and 1, 0.95 will display the 95 percent confidence regions, and 0 will not.

show

Display sample names, 1 = show names, 0 = do not show names.

grey.scale

Use grey-scale colors, 1 = grey-scale, 0 = not grey-scale.

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 scatter plot. The plot can be retrieved from within R via print(mSetObj$imgSet$pca.score2d_PCx_PCy.plot).

References

adapted from PlotPCA2DScore (https://github.com/xia-lab/MetaboAnalystR).

Author

Nicolas T. Wirth mail.nicowirth@gmail.com Technical University of Denmark License: GNU GPL (>= 2)