graphHab {FactoInvestigate}

Colored factor graph

Description

Realised the graph of individuals colored after a variable categories

Usage

graphHab(res, file = "", dim = 1:2, hab = NULL, ellipse = TRUE, Iselec = "contrib", 
         Rselec = "cos2", Cselec = "contrib", Icoef = 1, Rcoef = 1, Ccoef = 1, 
         figure.title = "Figure", graph = TRUE, cex = 0.7, 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.

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.

Icoef

a numerical coefficient to adjust the individuals 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.

figure.title

the text label to add before graph title.

graph

a boolean : if TRUE, graphs are ploted.

cex

an optional argument for the generic plot functions, used to adjust the size of the elements plotted.

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 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 rows or the columns) numbered 1 to 5 are drawn.
- Iselec = c("name1","name5") then the individuals (respectively the rows or the columns) named name1 and name5 are drawn.
- Iselec = "contrib 10" then the 10 active or illustrative individuals (respectively 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 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 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 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 rows or the columns) that have the highest cos2 on the 2 dimensions of the plane are drawn.

The Icoef argument (respectively 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

factoGraph, graphInd, graphCA, graphVar, graphSup

Examples

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

## End(Not run)