Can you help me?

I can't figure out why all 6 genes are not showing up on the graph

define repressilator model

repressilator = function(times, x, p){

Extract the state variables

mlacI = x[1]
mtetR = x[2]
mcI = x[3]
placI = x[4]
ptetR = x[5]
pcI = x[6]

Extract the parameter values

alpha0 = p[1]
alpha = p[2]
beta = p[3]
n = p[4]

Evaluate the differential equations (at time t)

dmlacIdt = -mlacI + alpha/(1+(pcI)^n) + alpha0
dmtetRdt = -mtetR + alpha/(1+(placI)^n) + alpha0
dmcIdt = -mcI + alpha/(1+(ptetR)^n) + alpha0
dplacIdt = -beta*(placI-mlacI)
dptetRdt = -beta*(ptetR-mtetR)
dpcIdt = -beta*(pcI-mcI)

Combine into a single vector

dxdt = c(dmlacIdt,dmtetRdt,dmcIdt,dplacIdt,dptetRdt,dpcIdt)



#Begin Code for Setup and Execution of Function

Set up time vector

time = seq(0,250,10)

Set up vector of parameter values

alpha0 = 0
alpha = 50
beta = 0.2
n = 2
params = c(alpha0,alpha,beta,n) # Parameter Vector

Set initial values for state variables

mlacI0 = 0.2
mtetR0 = 0.1
mcI0 = 0.3
placI0 = 0.1
ptetR0 = 0.4
pcI0 = 0.5

states0 = c(mlacI0,mtetR0,mcI0,placI0,ptetR0,pcI0) # State Variable Vector

Now, Find Numerical Solutions to the ODE!

Function ode() takes in, in this order:

state variables, times vector, your ODE function name,

and parameters

numSolutions = ode(states0,time,repressilator,params)

Note that the ode() function returns a matrix with

the number of rows defined by the length of the time vector

and the number of columns equal to the number of state variables

plus one. The first column is the time points at which the function

is evaluated. The remaining columns are the solutions for each

state variable in the order defined by your ODE function.

Next, Plot Output from Model

matplot(numSolutions[,1], numSolutions[,2:3], type=c("l","l","l","l","l","l"),
lty=c(1,2), lwd=c(4,4), xlab="",ylab="",col=c("purple","pink","red","blue","green","orange"))

Add a legend in the top right corner with legend labels

legend('topleft',legend=c("mlacI0","mtetR0","mcI0","placI0","ptetR0","pcI0"), col=c("purple","pink","red","blue","green","orange"),
lty=c(1,2), lwd=c(4,4), cex=0.75)

Add a title and axes labels

title("Repressilator Model",xlab="time",ylab="Expression")


Welcome to the RStudio community!

In order for us to help you with your question, please provide us a minimal reproducible example where you provide a minimal (dummy) dataset and code that can recreate the issue. Once we have that, we can go from there. For help on creating a Reprex, see this guide:

Also, try to make your post title more informative :slight_smile:

Good luck!

This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.

If you have a query related to it or one of the replies, start a new topic and refer back with a link.