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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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 datasetsapply(depths, MyFun)->symbols#create the
vectors for the plotfiguresas.vector(symbols)->symbols
library(ape)col.vec<-symbolsplot(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
Vårkänslor? Hitta någon att dela dem med! MSN Dejting
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On Thu, 2008-08-07 at 16:15 +0300, Monna Nyg?rd wrote:> 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 >In order to run the example, we'll need some data, even if it is made up. I think you can get the values you want like this: x<-ceiling(x/100)> ...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?If you want to make colors darker, you can do something like this: darkenColor<-function(col,colorshift=0.75) { rgbmat<-col2rgb(col) ncol<-dim(rgbmat)[2] rgbmat<-rgbmat*colorshift return(rgb(rgbmat)) } This will darker your colors toward black. Jim