Visualization of meanQ files fastSTRUCTURE

[sekhwal]

Hi,
Could anyone please let me know the initial codes to start visualizing the meanQ files, generated from fastSTRUCTURE. I am totally lost in the tutorial of pophelper. It is very large and complicate.

[royfrancis]

Here is a short example. You can run this yourself and it should work on your system.

library(pophelper)

# get a list of run files
f <- list.files(path=system.file("files/faststructure",package="pophelper"), full.names=T)

# read them in
flist <- readQ(files=f)

# plot one of the runs
plotQ(qlist=flist[3],exportpath=getwd())

This exports a figure to your working directory. When reading your own files, change the first line to a folder containing your files.

f <- list.files(path="path/to/your/files", full.names=T)

[sekhwal]

Hi,
Thank you for your reply. However, it show still error:

library(pophelper)

f <- list.files(path=system.file("E:/TASSEL-work/SEGI/popheler/", package="pophelper"), full.names=T)

flist <- readQ(files=f)

error:

Error in readQ(files = f) : readQ: No input files.

[sekhwal]

Please let me know how to access my own files generated by faststructure.

[royfrancis]

As I said in the last line, for your own files, you should use

f <- list.files(path="E:/TASSEL-work/SEGI/popheler/", full.names=T)

without system.file.

[sekhwal]

Hi, it works. Now, I am trying to add metadata in my plot. I tried in different ways to figure out but I am not able to get a plot with label information. Here is my code: threelabset <- read.delim("E:/pophe/SEGI_pop.txt", header=T, stringsAsFactors=F) head(threelabset) nrow(threelabset) sapply(threelabset, is.character) onelabset <- threelabset[,1,drop=FALSE] #Sorting with group labels segi_p1 <- plotQ(qlist=segi_flist[c(1, 2, 3, 4)],imgoutput="join",returnplot=T,exportplot=F,basesize=11, grplab=onelabset, grplabsize=3.5,linesize=0.8,pointsize=3, sharedindlab=F,sortind="all") segi_p1 message : $data $data$qlist [1] NA $data$grplab [1] NA