# 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){
with(as.list(c(state,parameters)),{

mlacI = x
mtetR = x
mcI = x
placI = x
ptetR = x
pcI = x

alpha0 = p
alpha = p
beta = p
n = p

# 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)

``````list(c(dxdt))
``````

})
}

#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

# and parameters

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

# 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")

Hi,

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 Good luck!
PJ

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