Introduction to Biological Data Analysis

TP 3: Graphics and data.frames

Prof. Patrick Meyer

BioSys Lab - Université de Liège

Simple graphics

1. pairs(CO2[,-1])
   
   Watch explanation:
   
   

2. pdf("myfirstplot.pdf")
   plot(CO2$conc,CO2$uptake)
   title("Uptake in function of the concentration in CO2")
   lines(c(30,1000),c(5,45),col="green",lty=3)
   dev.off()
   

   
   Watch explanation:
   
   And for the pdf:
   
   

data.frame

1. write.table(CO2,file="mydata.txt",sep=",")
   mydata <- read.table("mydata.txt",sep=",",header=T)
   

   
   Watch explanation:
   
   

2. sum(CO2$Type=="Quebec" & CO2$uptake>35 & CO2$Treatment=="chilled")

   
   Watch explanation:
   
   

3. index <- which(CO2$conc==min(CO2$conc))
   which(CO2$uptake==max(CO2$uptake[index]))
   

   
   Watch explanation:
   
   
   

4. maxuptake <- function(nameplant){
     max(CO2$uptake[CO2$Plant==nameplant])
   }
   maxvec <- sapply(levels(CO2$Plant),maxuptake)
   

   
   Watch explanation:
   
   

Advanced graphics

1. minuptake <- function(nameplant){
     min(CO2$uptake[CO2$Plant==nameplant])
   }
   minmaxmat <- rbind(sapply(levels(CO2$Plant),minuptake),maxvec)
   barplot(minmaxmat,beside=T,col=c("red","blue"),main="minima and maxima of uptakes by plant")
   

   
   Watch explanation:
   
   

2. uptakemat <- matrix(CO2$uptake,nr=7)
   rownames(uptakemat) <- CO2$conc[1:7]
   colnames(uptakemat) <- unique(CO2$Plant)
   heatmap(uptakemat,Rowv=NA,Colv=NA)
   

   
   Watch explanation:
   
   

3. par(mfrow=c(1,2))
   plot(CO2$conc,CO2$uptake)
   barplot(minmaxmat,beside=T,col=c("red","blue"),main="minima and maxima of uptakes by plant")
   

   
   Watch explanation:
   
   

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