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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