
Hi all.

I would be very pleased if someone could help me, as I do not seem to get the different branches of my tree painted in different colours. The closest I get is colouring the names of my samples(=names of the branches). Here is the code.






data <- read.table(file = "S://SEDIM//TRFLP//B12.5_50-700bp.txt" , as.is = TRUE, header = TRUE, sep = "\t", row.names = 1)#define vector with depths of samples









row.names(data)<-



 c("119","175","135","330","51","422","67.0","409","470.0","70","67","89","134.5","215","330.0","409.0","470","50.5","80","119.0","174.5","222","301","421.5","280","171","256","243","404","37","157","28","187.0","79.5","42.0","283","261","85","147","204.0","235","411.0","514","77","204","87","366","306","351","371","38","534","199","407","42","167","480","195","22","35","80.0","433","43","109","214","363","292","61","115","178","273","521","72","126","253","288","501","82.5","113","250","359.0","498","19","130","389","324","24","58","124","388","319.0","164.0","101.0","153","383","345","219","179","161","375","298","450.0","555","439","54","54.5","490","465","411","18.0","85.0","503","455","394","179.0","187","416","447","219.0","461","164","366.0","474","167.0","236","507","319","509","467","507.5","450","359","507.0","192","453","101","456","512","517")

 depths <- c("119","175","135","330","51","422","67.0","409","470.0","70","67","89","134.5","215","330.0","409.0","470","50.5","80","119.0","174.5","222","301","421.5","280","171","256","243","404","37","157","28","187.0","79.5","42.0","283","261","85","147","204.0","235","411.0","514","77","204","87","366","306","351","371","38","534","199","407","42","167","480","195","22","35","80.0","433","43","109","214","363","292","61","115","178","273","521","72","126","253","288","501","82.5","113","250","359.0","498","19","130","389","324","24","58","124","388","319.0","164.0","101.0","153","383","345","219","179","161","375","298","450.0","555","439","54","54.5","490","465","411","18.0","85.0","503","455","394","179.0","187","416","447","219.0","461","164","366.0","474","167.0","236","507","319","509","467","507.5","450","359","507.0","192","453","101","456","512","517")#function for labelling plotting figures

MyFun <- function(x){

          if
(x < 100) {

                   x
<- 1

}

          if
(x > 100 & x < 200){

                   x
<- 2

} 

          if
(x > 200 & x < 300){

                   x
<- 3

} 

          if
(x > 300 & x < 400){

                   x
<- 4

} 

          if
(x > 400 & x < 500){

                   x
<- 5

} 

          if
(x > 500){

                   x
<- 6

          }

          return((x))

}




#apply the function to the dataset

sapply(depths, MyFun)->symbols

 

#create the vectors for the plotfigures

as.vector(symbols)->symbols



library(ape)

col.vec<-symbols



plot(as.phylo(hclust(dist((data)))),tip.color=col.vec,main=" Hierarchical
cluster analysis ") I need to change the tip.color into something else, but what?Even better would be if someone could help me changing the colours given according to the depth of the sample (according to how high a number I have given the samples in row.names), I mean getting darker as the samples get deeper etc.. Is there an easy way doing this?

Thank you so much in advance,all help appreciated.
Regards, Yvonne
 

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