plot_PCA: plot_PCA: replacement for plot.PCA

In HanOostdijk/HOQCutil: Utilities by Han Oostdijk

plot_PCA: replacement for plot.PCA

Description

plot_PCA is a replacement for plot.PCA. Out of this function I took the functionality that I need and added the functionality to emphasize points (variables or individuals). The function plots the variables or individuals information from the structure returned by the function PCA.

Usage

plot_PCA(
  res,
  var_ind = "ind",
  axes = 1:2,
  cex = 1,
  font.std = 1,
  pch.std = 20,
  col.std = "black",
  font.emp = 2,
  pch.emp = pch.std,
  col.emp = "red",
  font.sel = font.std,
  pch.sel = pch.std,
  col.sel = col.std,
  font.sup = 3,
  pch.sup = 1,
  col.sup = "blue",
  show.sup = TRUE,
  select = NULL,
  emphasize = NULL,
  invisible = NULL
)

Arguments

res	Structure that is the output of the function PCA
var_ind	Character string that indicates if variables (var) or individuals (ind) will be plotted. Default: "ind"
axes	Numeric vector with two integers indicating the dimensions that will be plotted. Default: 1:2
cex	Positive number indicating the size of symbols and labels. Default: 1
font.std	Positive integer indicating the font that is used for the standard labels (i.e. not for supplemental, selected or emphasized elements). See description of par() for details: 1 plain text, 2 bold face, 3 italic and 4 bold italic. Default: 1
pch.std	Positive integer indicating the plotting character that is used for the standard points (i.e. not for supplemental, selected or emphasized elements). See description of points for details: 0 open square, 1 open circle, 2 open triangle etc. Default: 20 (i.e. very small closed circle)
col.std	Color specification for the standard elements (i.e. not for supplemental, selected or emphasized elements). See description of par() for details of specification. Default: "black"
font.emp	Positive integer indicating the font that is used for the labels of emphasized elements. See description of font.std. Default: 2
pch.emp	Positive integer indicating the plotting character that is used for the emphasized points. See description of pch.std. Default: pch.std
col.emp	Color specification for emphasized elements. See description of col.std. Default: "red"
font.sel	Positive integer indicating the font that is used for the labels of selected elements. See description of font.std. Default: font.std
pch.sel	Positive integer indicating the plotting character that is used for the selected points. See description of pch.std. Default: pch.std
col.sel	Color specification for selected elements. See description of col.std. Default: col.std
font.sup	Positive integer indicating the font that is used for the labels of supplemental elements. See description of font.std. Default: 3
pch.sup	Positive integer indicating the plotting character that is used for the supplemental points. See description of pch.std. Default: 1
col.sup	Color specification for supplemental elements. See description of col.std. Default: "blue"
show.sup	Boolean indicating if supplemental elements should be shown. Default: TRUE
select	Character string with a selection criterion (see details) or an integer vector with the sequence numbers of the active elements that are selected (i.e. be given a different layout than the other elements). Default: NULL (i.e. all are selected)
emphasize	Character vector with the rownames or an integer vector with the sequence numbers of the active elements that should be emphasized (i.e. be given a different layout than the other elements). Default: NULL (i.e. none are emphasized)
invisible	Character vector with the rownames of the elements (active and supplemental) that are not shown. Default: NULL

Details

The select mechanism is taken over asis from the FactoMineR::PCA function. The labels of selected elements will be plotted.
The authors Francois Husson [e-mail] and Jeremy Mazet describe it as follows:

The select argument can be used in order to select a part of the elements (individuals if you draw the graph of individuals, or variables if you draw the graph of variables) that are drawn. For example, you can use:
select = 1:5 and then the elements 1:5 are drawn.
select = c("name1","name5") and then the elements that have the names name1 and name5 are drawn.
select = "coord 10" and then the 10 elements that have the highest (squared) coordinates on the 2 chosen dimensions are drawn.
select = "contrib 10" and then the 10 elements that have the highest contribution on the 2 dimensions of your plot are drawn.
select = "cos2 5" and then the 5 elements that have the highest cos2 on the 2 dimensions of your plot are drawn.
select = "dist 8" and then the 8 elements that have the highest distance to the center of gravity are drawn.

NB. the following functionality is contained in plot.PCA but not described there:
select = "cos2 0.8" and then the elements for which the sum of the cos2 on the 2 dimensions of your plot is greater than 0.8 are drawn.

Acknowledgements

All ideas come from the creators of the FactoMineR package. This implementation is mine and if you find any errors, these will be mine. In case of errors try using the original plot.PCA.

Examples

## Not run: 
plot_PCA(res,cex=0.8,show.sup = F,emphasize = 'BU03620304',sel='contrib 6')

## End(Not run)

HanOostdijk/HOQCutil documentation built on July 28, 2023, 5:56 p.m.