factoGraph {FactoInvestigate}

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)