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royfrancis / pophelper

An R package to analyse and visualise admixture proportions from STRUCTURE, fastSTRUCTURE, TESS, ADMIXTURE etc.
http://royfrancis.github.io/pophelper/
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Change sample names in plotQMultiline #3

Closed markusruhsam closed 7 years ago

markusruhsam commented 7 years ago

Hello,

I was wondering if it's possible to have the actual sample names in the multi-line plot instead of the numbers?

Thank you

Markus

image

royfrancis commented 7 years ago

By default, it labels numerically 1, 2, 3 ... If you set the option useindlab=T, then labels are taken from input list object. The rownames of the list object are used as individual names. Here is a working example below:

library(pophelper)

#read structure file
sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=T)
slist <- readQ(files=sfiles[1])

# plot using numeric numbering
plotQMultiline(slist,useindlab=F)

#plot using labels from the input (no change because input rownames are 1, 2, 3 ...)
plotQMultiline(slist,useindlab=T)

#read new labels
inds <- read.delim(system.file("files/structureindlabels.txt",package="pophelper"),header=FALSE,stringsAsFactors=FALSE)

# add labels as rownames to qlist
rownames(slist[[1]]) <- inds$V1

# plot with new labels.
plotQMultiline(slist,useindlab=T)

# plot without using labels from input.
plotQMultiline(slist,useindlab=F)
markusruhsam commented 7 years ago

That’s great. Thank you!

Markus

From: Roy Francis [mailto:notifications@github.com] Sent: 23 January 2017 17:46 To: royfrancis/pophelper Cc: Markus Ruhsam; Author Subject: Re: [royfrancis/pophelper] Sample names (#3)

By default, it labels numerically 1, 2, 3 ... If you set the option useindlab=T, then labels are taken from input list object. The rownames of the list object are used as individual names. Here is a working example below:

library(pophelper)

read structure file

sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=T)

slist <- readQ(files=sfiles[1])

plot using numeric numbering

plotQMultiline(slist,useindlab=F)

plot using labels from the input (no change because input rownames are 1, 2, 3 ...)

plotQMultiline(slist,useindlab=T)

read new labels

inds <- read.delim(system.file("files/structureindlabels.txt",package="pophelper"),header=FALSE,stringsAsFactors=FALSE)

add labels as rownames to qlist

rownames(slist[[1]]) <- inds$V1

plot with new labels.

plotQMultiline(slist,useindlab=T)

plot without using labels from input.

plotQMultiline(slist,useindlab=F)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/royfrancis/pophelper/issues/3#issuecomment-274562434, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AWI7FrD3UdyXshzO5LOU7WUkoT7QN4G3ks5rVOdbgaJpZM4LrH3M.

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markusruhsam commented 7 years ago

Hi Roy,

I just ran through the script with the following commands but the plot still had only the rownames in the plot.

setwd(choose.dir()) library(pophelper) Loading required package: Cairo Loading required package: ggplot2 pophelper v2.0.0 ready. sfiles <- choose.files() slist <- readQ(files=sfiles) inds <- read.delim("mylabels.txt",header=FALSE,stringsAsFactors=FALSE) rownames(slist[[1]]) <- inds$V1 plotQMultiline(slist[c(6)], lpp=7, spl=70, useindlab=T, imgtype="pdf") 20000_run_6_f-Multiline-1.pdf exported.

Maybe it’s because I didn’t use system.file when using read.delim but I couldn’t get it to work. I am not familiar with system.files but thought that "files/structureindlabels.txt" should be substituted with the path to my label files but

inds <- read.delim(system.file("Z:/My Documents/LAB/LAB BOOK/Bluebells/SNP ARRAY/Analyses/pophelper/mylabels.txt", package="pophelper"),header=FALSE,stringsAsFactors=FALSE) produced this error

Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input In addition: Warning message: In file(file, "rt") : file("") only supports open = "w+" and open = "w+b": using the former

Thank you

Markus

From: Roy Francis [mailto:notifications@github.com] Sent: 23 January 2017 17:46 To: royfrancis/pophelper Cc: Markus Ruhsam; Author Subject: Re: [royfrancis/pophelper] Sample names (#3)

By default, it labels numerically 1, 2, 3 ... If you set the option useindlab=T, then labels are taken from input list object. The rownames of the list object are used as individual names. Here is a working example below:

library(pophelper)

read structure file

sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=T)

slist <- readQ(files=sfiles[1])

plot using numeric numbering

plotQMultiline(slist,useindlab=F)

plot using labels from the input (no change because input rownames are 1, 2, 3 ...)

plotQMultiline(slist,useindlab=T)

read new labels

inds <- read.delim(system.file("files/structureindlabels.txt",package="pophelper"),header=FALSE,stringsAsFactors=FALSE)

add labels as rownames to qlist

rownames(slist[[1]]) <- inds$V1

plot with new labels.

plotQMultiline(slist,useindlab=T)

plot without using labels from input.

plotQMultiline(slist,useindlab=F)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/royfrancis/pophelper/issues/3#issuecomment-274562434, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AWI7FrD3UdyXshzO5LOU7WUkoT7QN4G3ks5rVOdbgaJpZM4LrH3M.

The Royal Botanic Garden Edinburgh is a charity registered in Scotland (No SC007983)

royfrancis commented 7 years ago

The system.file() is not needed if reading a file locally.

The below should work.

 sfiles <- choose.files()
 slist <- readQ(files=sfiles)
 inds <- read.delim("mylabels.txt", header=FALSE, stringsAsFactors=FALSE)
 rownames(slist[[1]]) <- inds$V1
 plotQMultiline(slist, lpp=7, spl=70, useindlab=T, imgtype="pdf")

If not, then we need to inspect if inds$V1 actually has a vector of the correct labels. And ensure that the first qlist element is renamed correctly like this rownames(slist[[1]]). If this still doesn't work, then you can send me the files and I can have a look.

markusruhsam commented 7 years ago

Hi Roy,

inds$V1 has a vector of the correct labels and rownames(slist[[1]]) has been renamed correctly but still no individual names in the plot. I attached the files – maybe you can have a look.

Thank you

Markus

From: Roy Francis [mailto:notifications@github.com] Sent: 24 January 2017 17:47 To: royfrancis/pophelper Cc: Markus Ruhsam; Author Subject: Re: [royfrancis/pophelper] Change sample names in plotQMultiline (#3)

The system.file() is not needed if reading a file locally.

The below should work.

sfiles <- choose.files()

slist <- readQ(files=sfiles)

inds <- read.delim("mylabels.txt", header=FALSE, stringsAsFactors=FALSE)

rownames(slist[[1]]) <- inds$V1

plotQMultiline(slist, lpp=7, spl=70, useindlab=T, imgtype="pdf")

If not, then we need to inspect if inds$V1 actually has a vector of the correct labels. And ensure that the first qlist element is renamed correctly like this rownames(slist[[1]]). If this still doesn't work, then you can send me the files and I can have a look.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/royfrancis/pophelper/issues/3#issuecomment-274880223, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AWI7FpVqNQY98-2hs5hCxW3knqa60AR_ks5rVjj4gaJpZM4LrH3M.

The Royal Botanic Garden Edinburgh is a charity registered in Scotland (No SC007983)

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royfrancis commented 7 years ago

I can't seem to find any attachments.

markusruhsam commented 7 years ago

As the files were attached to the last email but obviously didn’t come through I re-sent the files to your email address given in the pophelper paper.

From: Roy Francis [mailto:notifications@github.com] Sent: 25 January 2017 11:07 To: royfrancis/pophelper Cc: Markus Ruhsam; Author Subject: Re: [royfrancis/pophelper] Change sample names in plotQMultiline (#3)

I can't seem to find any attachments.

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royfrancis commented 7 years ago

Sorry for the delay, but your files do seem to work for me. I tried one file. I used the code below. See attached figure.

library(pophelper)

#read structure file
slist <- readQ(files="20000_run_6_f")

# plot using numeric numbering
plotQMultiline(slist,useindlab=F)

#read new labels
inds <- read.delim("mylabels.txt",header=FALSE,stringsAsFactors=FALSE)

# add labels as rownames to qlist
rownames(slist[[1]]) <- inds$V1

# plot with new labels.
plotQMultiline(slist,useindlab=T)

20000_run_6_f-multiline-1

markusruhsam commented 7 years ago

I just worked out why it didn’t work as I used

slist <- readQ(files=sfiles) inds <- read.delim("mylabels.txt",header=FALSE,stringsAsFactors=FALSE) rownames(slist[[1]]) <- inds$V1 plotQMultiline(slist[c(6)], lpp=7, spl=70, useindlab=T, imgtype="pdf")

when I should have replaced the 1 in rownames(slist[[1]]) with 6 as I instructed the program to plot the 6th run in plotQMultiline()

slist <- readQ(files=sfiles) inds <- read.delim("mylabels.txt",header=FALSE,stringsAsFactors=FALSE) rownames(slist[[6]]) <- inds$V1 plotQMultiline(slist[c(6)], lpp=7, spl=70, useindlab=T, imgtype="pdf")

Thanks for your help

Markus

From: Roy Francis [mailto:notifications@github.com] Sent: 27 January 2017 16:50 To: royfrancis/pophelper Cc: Markus Ruhsam; Author Subject: Re: [royfrancis/pophelper] Change sample names in plotQMultiline (#3)

Sorry for the delay, but your files do seem to work for me. I tried one file. I used the code below. See attached figure.

library(pophelper)

read structure file

slist <- readQ(files="20000_run_6_f")

plot using numeric numbering

plotQMultiline(slist,useindlab=F)

read new labels

inds <- read.delim("mylabels.txt",header=FALSE,stringsAsFactors=FALSE)

add labels as rownames to qlist

rownames(slist[[1]]) <- inds$V1

plot with new labels.

plotQMultiline(slist,useindlab=T)

[https://cloud.githubusercontent.com/assets/5083500/22379296/02c777b0-e4b9-11e6-8691-a8c6ec6bcffc.png]https://cloud.githubusercontent.com/assets/5083500/22379296/02c777b0-e4b9-11e6-8691-a8c6ec6bcffc.png

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