
Hi all,

 

I'm making a PCA plot with eight variables (columns taken from a larger data frame "fieldTrial0809[idx,c(39:46)]"). I then want the symbols in the plot to be colored as a gradient from red to blue, depending on the value of another column in "fieldTrial0809[idx, c(48)]" containg temperatures from -12.1 to -5.4.

 

I don't want to use the heat.colors(n) function, because then I just get colors from red to yellow...

 

I've created a vector "colTemperature" with 12 colors and I've also made a new vector "tempACC", based on the values of "fieldTrial0809[idx, c(48)]" with 12 levels.

 

What I don't know, is how to incorporate this vector in the text() function below:


> df=fieldTrial0809[idx,c(39:46)]
> PC=prcomp (df[,1:8])
> hcl=hclust(dist(df))

> plot(PC$x[,1],PC$x[,2], col="white", main="8 variables")
> text(PC$x[,1],PC$x[,2], labels=cutree(hcl,8), col=cutree(hcl,8))   # Change this, but how???

>

> col1=rgb(0.164,0.043,0.850)   # Set the colors
> col2=rgb(0.150,0.306,1.000)
> col3=rgb(0.250,0.630,1.000)
> col4=rgb(0.450,0.853,1.000)
> col5=rgb(0.670,0.973,1.000)
> col6=rgb(0.880,1.000,1.000)
> col7=rgb(1.000,1.000,0.750)
> col8=rgb(1.000,0.880,0.600)
> col9=rgb(1.000,0.679,0.450)
> col10=rgb(0.970,0.430,0.370)
> col11=rgb(0.850,0.150,0.196)
> col12=rgb(0.650,0.000,0.130)
> colTemperature=c(col1,col2,col3,col4,col5,col6,col7,col8,col9,col10,col11,col12)   # Put all colors in a vector
> 
> tempLT50_ACC=fieldTrial0809[idx, c(48)]
> tempACC=cut(tempLT50_ACC, breaks=c(-5.4, -5.958333333, -6.516666667, -7.075, -7.633333333, -8.191666667, -8.75, -9.308333333, -9.866666667, -10.425, -10.98333333, -11.54166667,-12.1))   # Define the breaks
> table(tempACC)
tempACC
(-12.1,-11.5]   (-11.5,-11]   (-11,-10.4] (-10.4,-9.87] (-9.87,-9.31] (-9.31,-8.75] 
           25            21            24            21           131            28 
(-8.75,-8.19] (-8.19,-7.63] (-7.63,-7.08] (-7.08,-6.52] (-6.52,-5.96]  (-5.96,-5.4] 
           33            14            11             7            17            11 

 

Finally, I've got another question, how do you decide how many components to use in "text(... labels=cutree(hcl,8), ...)"? Do you try with  different values until i looks nice or what..?

 

Best regards,

 

Joel
 		 	   		  
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