The following lines are executed very well.

Condition<-factor(c("ARef","ARef","CO2","CO2","Light","Light","NaCl","NaCl","NaNO3","NaNO3","pH","pH","Temp","Temp"))

Time<- factor(c("1", "24","1", "24", "1", "24", "1", "24", "1", "24","1", "24", "1", "24"))
data.frame(Sample=colnames(RG),Condition,Time)
design <-model.matrix(~~Condition+Time)
rownames(design)<-colnames(RG)
design

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Now, I would like to create the following plots:

1) The # of false discoveries vs the # of genes selected for the Fisher test (total reads) and the Fisher test (TMM)

2)  The # of false discoveries vs the # of genes selected for the Poisson-Exact and Poisson-LR-TMM normalized with my datasets.

Any helpful to perform these plots will be appreciated.