flux.dome.graphics: Plot of the flux dome
In SimEvolEnzCons: Simulation of Evolution of Enzyme Under Constraints

Description Usage Arguments Details Value See Also Examples

Function flux.dome.graph3D gives a 3D graph of flux dome for a three-enzyme pathway.

Function flux.dome.projections gives a triangular diagram of flux dome, and if add.reg==TRUE, it also gives a plot of the curve defined by the intersection of the dome with the upright plan drawn from regulation line.

flux.dome.graph3D(A_fun,Etot_fun,add.reg=FALSE,B_fun=NULL,
E_ini_fun=NULL,X_fun=1,marge_section=0.1,marge_top.dome=0.5)

flux.dome.projections(A_fun,Etot_fun,add.reg=FALSE,B_fun=NULL,
E_ini_fun=NULL,X_fun=1,nbniv=9,niv.palette=NULL,marge_section=0.1,
posi.legend="topleft",new.window=FALSE,cex.pt=1.5,...)

`A_fun`	Numeric vector of activities
`Etot_fun`	Numeric value of total concentration
`add.reg`	Logical. Add regulation line in plots? Default is `FALSE`.
`B_fun`	Numeric vector of global co-regulation coefficients. Same length as `E_ini_fun`.
`E_ini_fun`	Numeric vector of initial concentrations
`X_fun`	Numeric value. Default is `1`
`marge_section`	Numeric. Height of section up to surface dome. Default is `0.1`
`marge_top.dome`	Numeric. Space between top dome and max of zlim. Default is `0.5`
`nbniv`	Numeric. Number of contour lines, between 3 and 11. Default is `9`
`niv.palette`	Character vector. Color palette to be passed to contour lines.
`posi.legend`	Contour line legend position. See details.
`new.window`	Logical. Does graphics appear in a new window ? Default is `TRUE`
`cex.pt`	Numeric. Size of points in plot(s) drawn by `flux.dome.projections`
`...`	Arguments to be passed to `plot` function, such as `lwd` or `cex.axis`

General

Available only for three-enzyme pathway, i.e. length of A_fun equal to 3.

Flux dome exists only in case of the competition.

E_ini_fun is rescaled by a cross product to have sum of E_ini_fun equal to Etot_fun.

Only flux dome is returned if add.reg is FALSE.

If add.reg=TRUE, E_ini_fun and B_fun are required. Else, default is NULL.

Function flux.dome.graph.3D

If add.reg is TRUE, a section corresponding to the upright plan drawn from line on which the relative concentrations move when there is co-regulations (see droites) is added on graph.

Function flux.dome.projections

Projection on plan (e1,e2,e3) is from blue for low flux to red for high flux. Colors are taken from Spectral palette of the package 'RColorBrewer'.

Because contour lines are calibrated to correspond to integer values of flux, it is possible to have a difference between input and output nbniv.

If add.reg is TRUE, line on which the relative concentrations move when there is co-regulations (see droites) is added on triangular diagram. Also, a new plot of the curve defined by the intersection of the dome with the upright plan drawn from this line is drawn.

Color palette for contour lines

By default, color palette for contour lines is taken in palette "Spectral" of package RColorBrewer, with cool colors for low flux values and warm colors for high ones.

Input your own color palette in niv.palette.

If color numbers in niv.palette is inferior to the number of contour lines nbniv, a warning message is printed and palette is replicated to have enough colors.

posi.legend is the position of the legend for contour line. It is a character vector of length 1 ("topleft", etc.) or a numeric vector of length 2, which is the coordinates of the upper left corner of the legend box. If NULL, the legend will not be shown. The first (resp. second) element of posi.legend is passed to argument x (resp. y). Note that the minimum and maximum coordinates for the return triangular plot are between -0.864 and 0.864 for x-axis, and -0.66 and 1.064 for y-axis. Use locator(1) to adjust position legend.

Function flux.dome.graph3D returns a 3D-graph of flux dome, with section in case of regulation.

Function flux.dome.projections returns a triangular diagram corresponding to the projection of the flux dome on the plan of relative concentrations. In the case of regulation (add.reg=TRUE), a straight line is drawn. If add.reg=TRUE, function flux.dome.projections also returns a plot of the curve defined by the intersection of the dome with the upright plan drawn from regulation line.

See function droites to compute regulation line.

Etot <- 100
A <- c(1,10,30)
beta <- matrix(c(1,10,5,0.1,1,0.5,0.2,2,1),nrow=3)
B <- compute.B.from.beta(beta)

#or for B :
B <- 1/c(0.2,0.5,0.3)
E0<- c(30,30,30)

flux.dome.graph3D(A,Etot,add.reg=TRUE,B,E0)
flux.dome.projections(A,Etot,add.reg=TRUE,B,E0)


#Position of legend at right
flux.dome.projections(c(1,10,30),100,posilegend=c(0.55,0.9))