factoGraph: Factorial graphs

In FactoInvestigate: Automatic Description of Factorial Analysis

Factorial graphs

Description

Realise all optimised factorial graphs

Usage

factoGraph(res, file = "", dim = 1:2, hab = NULL, ellipse = TRUE, Iselec = "contrib", 
           Vselec = "cos2", Rselec = "cos2", Cselec = "cos2", Mselec = "cos2", 
           Icoef = 1, Vcoef = 1, Rcoef = 1, Ccoef = 1, Mcoef = 1, 
           figure.title = "Figure", graph = TRUE, cex = 0.7, 
		   codeGraphInd = NULL, codeGraphVar = NULL ,codeGraphCA = NULL, 
		   options = NULL)

Arguments

res	an object of class PCA, CA or MCA
file	the file path where to write the description in Rmarkdown language. If not specified, the description is written in the console.
dim	a 2 dimensional numerical vector giving the factorial dimensions to use for the representation (by default the first plane)
hab	a variable name or index to use to color the individuals (or rows) among the variable categories.
ellipse	a boolean : if TRUE, ellipses are plotted with the coloration of individuals (or rows).
Iselec	the individuals to select ; see the details section
Vselec	the variables to select ; see the details section
Rselec	the rows to select (for a CA res object) ; see the details section
Cselec	the columns to select (for a CA res object) ; see the details section
Mselec	the supplementary variables to select ; see the details section
Icoef	a numerical coefficient to adjust the individuals selection rule ; see the details section
Vcoef	a numerical coefficient to adjust the variables selection rule ; see the details section
Rcoef	a numerical coefficient to adjust the rows selection rule (for a CA res object) ; see the details section
Ccoef	a numerical coefficient to adjust the columns selection rule (for a CA res object) ; see the details section
Mcoef	a numerical coefficient to adjust the supplementary variables selection rule ; see the details section
figure.title	the text label to add before graph title
graph	a boolean : if TRUE, graphs are plotted.
cex	an optional argument for the generic plot functions, used to adjust the size of the elements plotted.
codeGraphInd	a character string corresponding to the code to use for the individuals graph.
codeGraphVar	a character string corresponding to the code to use for the variables graph.
codeGraphCA	a character string corresponding to the code to use for the CA graph.
options	a character string that gives the output options fir the figures. If NULL, options="r, echo = FALSE, fig.align = 'center', fig.height = 3.5, fig.width = 5.5" for linux and Mac and options="r, echo = FALSE, fig.height = 3.5, fig.width = 5.5" for Windows

Details

The Iselec argument (respectively Vselec, Rselec or Cselec) is used in order to select a part of the elements that are drawn and described. For example, you can use either :
- Iselec = 1:5 then the individuals (respectively the variables, the rows or the columns) numbered 1 to 5 are drawn.
- Iselec = c("name1","name5") then the individuals (respectively the variables, the rows or the columns) named name1 and name5 are drawn.
- Iselec = "contrib 10" then the 10 active or illustrative individuals (respectively the variables, the rows or the columns) that have the highest contribution on the 2 dimensions of the plane are drawn.
- Iselec = "contrib" then the optimal number of active or illustrative individuals (respectively the variables, the rows or the columns) that have the highest contribution on the 2 dimensions of the plane are drawn.
- Iselec = "cos2 5" then the 5 active or illustrative individuals (respectively the variables, the rows or the columns) that have the highest cos2 on the 2 dimensions of the plane are drawn.
- Iselec = "cos2 0.8" then the active or illustrative individuals (respectively the variables, the rows or the columns) that have a cos2 higher to 0.8 on the plane are drawn.
- Iselec = "cos2" then the optimal number of active or illustrative individuals (respectively the variables, the rows or the columns) that have the highest cos2 on the 2 dimensions of the plane are drawn.

The Icoef argument (respectively Vcoef, Rcoef or Ccoef) is used in order to adjust the selection of the elements when based on Iselec = "contrib" or Iselec = "cos2". For example :
- if Icoef = 2, the threshold is 2 times higher, and thus 2 times more restrictive.
- if Icoef = 0.5, the threshold is 2 times lower, and thus 2 times less restrictive.

Author(s)

Simon Thuleau and Francois Husson

See Also

graphInd, graphHab, graphCA, graphVar, graphSup

Examples

require(FactoMineR)
data(decathlon)
res.pca = PCA(decathlon, quanti.sup = c(11:12), quali.sup = c(13), graph = FALSE)
## Not run: 
factoGraph(res.pca)

require(FactoMineR)
data(children)
res.ca = CA(children, row.sup = 15:18, col.sup = 6:8, graph = FALSE)
factoGraph(res.ca)

data(tea)
res.mca = MCA(tea, quanti.sup = 19,quali.sup = 20:36, graph = FALSE)
factoGraph(res.mca)

## End(Not run)

FactoInvestigate documentation built on Nov. 28, 2023, 1:10 a.m.