Re: [R] Replacing values in dataframes
Thank you so much for trying to help me.
Thus, I still can't get it to work.
I will clearify a bit. If you somehow have time helping me I would much
appreciate it.
NAD and Prot.amount are both data.frames. There are several different
dataframes called NAD,NAD1, NAD2 etc. that I would like to run the loop over.
Prot.amount has all the samplenames as its row.names and the correct values as
Prot.amount[,1]. Thus, the NADs are data.frames with values for the samples,
they DO NOT contain all the samples.
> NAD[1:3,1:3]
Sample.Id Main.abs..1 Main.abs..2
148 10a 0.04836 0.04994
167 11a_1109 0.32245 0.36541
173 11b_1109 0.29293 0.32815
> Prot.amount[1:3,1]
> 10a 11a_1109 11b_1109
15.516 38.248 42.297
> dim(Prot.amount)
[1] 30 1
> dim(NAD)
[1] 23 12
The thing I want to do is to replace the sample name with the correct
Prot.amount. So that in all dataframes where I have for instance sample 10a i
want to have a column with its corresponding prot.amount, here 15.516.
Sample.id=row.names(Prot.amount)
gives a vector with all the correct sample.id's
new.id=Prot.amount[1:nrow(Prot.amount),] gives all the samples and their
correct prot.amounts.
> new.id[1:8]
10a 11a_1109 11b_1109 12a_1109 12b_1109 1a_1109 2a 2a_1009
15.516 38.248 42.297 36.134 25.467 28.1849.9272.242
iddf <- data.frame((Sample.id=row.names(Prot.amount)),
new.id=Prot.amount[1:nrow(Prot.amount),])
Thus,
newNAD <- merge( NAD, iddf)
> newNAD[4,]
Sample.Id Main.abs..1 Main.abs..2 Main.abs..3 Main.abs..4 Main.abs..5
Main.abs..6 Main.abs..7 Main.abs..8 Main.abs..9
4 12a_1109 0.26291 0.26794 0.27809 0.28948 0.29654
0.3051 0.31388 0.3223 0.33066
Main.abs..10 Main.abs..11 X.Sample.id...row.names.Prot.amount.. new.id
4 0.33806 0.34577 10a 15.516
Produces the correct looking dataframe, only that the first sample.id and
corresponding Prot.amount gets merged to all rows.
So what I need to do is a loop. This is my suggestion:
Changing<-function(A){
tmp<-mat.or.vec(nr=nrow(A),nc=1)
newNAD <-mat.or.vec(nr=nrow(A),nc=1)
for (j in 1:nrow(A)) {
tmp[j] <- data.frame((A$Sample.id=row.names(Prot.amount)),
(A$new.id=Prot.amount[j,]))
newNAD <- merge(A[j,], tmp[j])
}
newNAD
}
Thus, of course it doesn't work that easily. This is becouse
> Changing(NAD)
Error in `$<-.data.frame`(`*tmp*`, "Sample.id", value = c("10a", "11a_1109", :
replacement has 30 rows, data has 23
meaning the dataframe NAD with the samples have 23 samples, the Prot.amounts
file have 30 different samples and their corresponding values. How do I include
into the loop that I only want to replace those Prot.amount values found in the
NAD dataframe?
Thank you so much!
> Date: Sat, 19 Sep 2009 21:35:31 -0700
> To: monn...@hotmail.com; r-help@r-project.org
> From: m...@llnl.gov
> Subject: Re: [R] Replacing values in dataframes
>
> What I would probably do is along these lines:
>
> iddf <- data.frame(Sample.id=names(Prot.amount), new.id=Prot.amount[1,])
>
> newNAD <- merge( NAD, iddf)
>
> This is not tested, but it looks right to me,
> assuming I understand the structure of what
> you're trying to do.
>
> I'm also assuming that NAD has more than three
> rows, and that Prot.amount has as many columns as
> NAD has rows. And that you just showed us the
> first three rows of NAD and first three columns
> of Prot.amount in order to keep the email simple.
>
> One final note ... if Prot.amount is an object
> within R, it is *not* a file. You may have read
> it in from a file, of course, but it isn't a file
> inside R. I'm assuming it's a dataframe.
>
> -Don
>
> At 1:18 PM +0300 9/19/09, Monna Nygård wrote:
> >Hi,
> >
> >
> >
> >This is a question of a newbie getting into the exciting world of R.
> >
> >
> >
> >I have several dataframes in the same format as NAD:
> >
> >
> >
> >
> >
> >> NAD[1:3,1:3]
> >
> > Sample.Id Main.abs..1 Main.abs..2
> >148 10a 0.04836 0.04994
> >167 11a_1109 0.32245 0.36541
> >173 11b_1109 0.29293 0.32815
> >
> >
> >What I want to do is to replace the Sample.Id
> >with a corresponding number.The number i have in
> >another file,called Prot.amount
> >
> >
> >
> >> Prot.amount[1:3,1]
> > 10a 11a_1109 11b_1109
> > 15.516 38.248 42.297
> >
> >
> >
> >
> >
> >> row.names(NAD)<-(NAD[,1])
> >> NAD$Sample.Id <- repla
[R] Replacing values in dataframes
Hi, This is a question of a newbie getting into the exciting world of R. I have several dataframes in the same format as NAD: > NAD[1:3,1:3] Sample.Id Main.abs..1 Main.abs..2 148 10a 0.04836 0.04994 167 11a_1109 0.32245 0.36541 173 11b_1109 0.29293 0.32815 What I want to do is to replace the Sample.Id with a corresponding number.The number i have in another file,called Prot.amount > Prot.amount[1:3,1] 10a 11a_1109 11b_1109 15.516 38.248 42.297 > row.names(NAD)<-(NAD[,1]) > NAD$Sample.Id <- replace(NAD$Sample.Id, > NAD$Sample.Id=="10a",Prot.amount["10a",1]) > NAD[1:3,1:3] Sample.Id Main.abs..1 Main.abs..2 10a 15.516 0.04836 0.04994 11a_1109 11a_1109 0.32245 0.36541 11b_1109 11b_1109 0.29293 0.32815 So what I have tried to do is to write a function that would allow me to replace the values automatically of all dataframes. This I just can't get to work. Thank you so much in advance! _ [[elided Hotmail spam]] [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] colouring a tree
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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[R] colouring a tree
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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[R] PCA analysis
Hi,
I have a problem with making PCA plots that are readable.
I would like to set different sympols instead of the numbers of my samples or
their names, that I get plotted (xlabs).
How is this possible? With points, i don´t seem to get the right data plotted
onto the PCA plot, as I do not quite understand from where it is taken. I dont
know how to
plot the correct columns of the prcomp outcome (p).
I would really appreciate if someone could help me, I have struggled with this
for days now. How can I make a function that gives different symbols
for the points, depending on how big the number given to it as xlabs is?
Making the plots.
read.table(file = "S:\\SEDIM\\TRFLP\\B90-700.txt",sep="\t", header=T)->boutbout
<-bout[-1]p <- prcomp(bout)
biplot(p, choices = c(2,3), scale = 1, pc.biplot = FALSE, var.axes = F, ylabs =
NULL,
xlabs=c("119","175","135","330","51","422","67","409","470","70","67","89","135","215","330","409","470","51","80","119","175","222","301","422","280","171","256","243","404","37","157","28","187","70","42","283","261","85","147","204","235","411","514","77","204","87","366","306","351","371","38","534","199","407","42","167","480","195","22","35","80","433","43","109","214","363","292","61","115","178","273","521","72","126","253","288","501","83","113","250","359","498","19","130","389","324","24","58","124","388","319","164","101","153","383","345","219","179","161","375","298","450","555","439","54","54","490","465","411","18","85","503","455","394","179","187","416","447","219","461","164","366","474","167","236","507","319","509","467","507","450","359","507","192","453","101","456","512","517"),
cex=0.67, main="90-700bp")
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[R] i-best, grep function
Hi,
I'm trying to use the i-best software. Does anyone have experience from this, I
can't get it to work with my data.
Here is the code:
T1 <- read.delim(file="S://SEDIM//Yvonne//2_5//T1.txt",col.names=
c("Dye/Sample_Peak", "Sample_File_Name", "Size", "Height", "Area_in_Point",
"Area_in_BP", "Data_Point", "Begin_Point","Begin_BP", "End_Point",
"End_BP", "Width_in_Point", "Width_in_BP", "User_Comments", "User_Edit"))
T1 <- subset(T1, Size < 1000 & Size > 50)
T1.B <- cbind(T1[grep("^B", as.character(T1$Color),perl=T),3],T1[grep("^B",
as.character(T1$Color),perl=T),5])
T1.B <- cbind(T1.B, T1.B[,2]/sum(T1.B[,2]))
It works alright until the last two lines. I try to grep the columns 3 and 5,
but the outcome is
T1.B
[,1] [,2].
I don´t quite understand the code of as.character(t1$Color), perl=T. Could
anyone please explane what this does, I havn´t found it anyware and I am so
stuck. Maybe I'm doing something else wrong as well..
I would really appreciate some help, thank you.
Yvonne
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[R] removing rows from matrix
Hi, I have a problem regarding matrix handeling. I am working with a serie of matrixes containing several columns. Now I would like to delete those rows of the matrixes,that in one of the columns contain values less than 50 or greater than 1000. How would this be possible, I have tried to create a simple function for this, but I just don't seem to get it right.Thank you so much for your help, Monna _ [[elided Hotmail spam]] PLink [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] missing values in document
No matter how I´ve tried o find a solution for this simple question, I can´t.
Sorry for bothering with such a matter.
I have an excel-files with some empty cells=missing values. How do I tell R
that these should be NA´s?
> TRFLP1 <-(read.table(file="S://SEDIM//Kokeilu//TRFLP1.txt",col.names=
> c("Dye_Sample Peak", "Sample_File_Name", "Size", "Height", "Area_in_Point",
> "Area_in_BP", "Data_Point", "Begin_Point", "Begin_BP", "End_Point", "End_BP",
> "Width_in_Point", "Width_in_BP", "1" ), header=F , dec = ",", )Error in
> scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line
> 1743 did not have 14 elements
I believe the error occurs becouse line 1743 has an empty cell. How do I read
in the file without first checking for missing values and changing them to NAs
myself?
Thank you for you time,
Monna Nygård
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