R/dialog.mehalocoa.cldetect.R
In yguitton/MeHaloCoA: Fast identification of Cl or Br containing compounds in LC-MS
# MeHaloCoA Tcl/Tk GUI for halogeneted compound search in MS data.
# Part of the code is based on the ade4TkGUI package by Jean Thioulouse <jthioulouse@biomserv.univ-lyon1.fr>, Stephane
# Dray <dray@biomserv.univ-lyon1.fr>
#cldetect function dialog frame
dialog.mehalocoa.cldetect <-
function(method="")
{
if(method==""){
#
# Main dialog window with title
#
tt <- tktoplevel()
tkwm.title(tt,"MeHaloCoA")
#
# Variables for text fields
#
outdirvar <- tclVar(as.character(getwd()))
matclvar<-tclVar("matcl")
#
# Variable for number fields
#
xsAnnotatevar<-tclVar("an")
plotpsvar<-tclVar("TRUE")
deprofvar<-tclVar("FALSE")
#clppmerrvar<-tclVar(50)
Threshvar<-tclVar(20)
m1var<-tclVar(1.003)
m2var<-tclVar(1.997)
mdiffvar<-tclVar(0.05)
ppmerrvar<-tclVar(50)
valvar<-tclVar("maxo")
mdiff2var<-tclVar(0.001)
myfilevar<-tclVar("halo_list.csv")
myfile2var<-tclVar("halo_list_short.csv")
m1needvar<-tclVar("FALSE")
#
# Title
#
TFrame <- tkframe(tt, relief="groove")
labh <- tklabel(TFrame, bitmap="questhead")
tkgrid(tklabel(TFrame,text="MeHaloCoA::cldetect", font="Times 18", foreground="red"), labh)
tkbind(labh, "<Button-1>", function() print(help("cldetect")))
tkgrid(TFrame)
#
# In and Out directories (option = files paths)
#
IOFrame <- tkframe(tt, relief="groove", borderwidth=2)
tkgrid(tklabel(IOFrame,text=" - Input & Output files -", foreground="blue"), columnspan=8)
outdir.entry <- tkentry(IOFrame, textvariable=outdirvar, width=55)
"delinsert"<-function(arg,title1){
tkdelete(arg, 0, "end")
tkinsert(arg, "end", tclvalue(tkchooseDirectory(initialdir=getwd(),title=title1)))
}
choosedir.but2 <- tkbutton(IOFrame, text="Browse",command=function() delinsert(arg=outdir.entry, title1="Your Result Directory"))
tkgrid(tklabel(IOFrame,text="Output path (outdir) : "), outdir.entry,choosedir.but2,tklabel(IOFrame,text="Path for Results "), sticky="w")
tkgrid(IOFrame, sticky="we")
#settings list for halogen detection algorithm
# "xsAnnotate" "plotps" "deprof" "clppmerr" "Thresh" "m1" "m2" "mdiff" "ppmerr"
# "val" "mdiff2" "myfile" "myfile2"
PARAMFrame <- tkframe(tt, relief="groove", borderwidth=2)
tkgrid(tklabel(PARAMFrame,text=" - cldetect Parameters -", foreground="blue"), columnspan=8)
xsAnnotate.entry <- tkentry(PARAMFrame, textvariable=xsAnnotatevar, width=6, state="normal")
plotps.entry <- tkentry(PARAMFrame, textvariable=plotpsvar, width=6, state="normal")
deprof.entry <- tkentry(PARAMFrame, textvariable=deprofvar, width=6, state="normal")
#clppmerr.entry <- tkentry(PARAMFrame, textvariable=clppmerrvar, width=6, state="normal")
Thresh.entry <- tkentry(PARAMFrame, textvariable=Threshvar, width=6, state="normal")
m1.entry <- tkentry(PARAMFrame, textvariable=m1var, width=6, state="normal")
m2.entry <- tkentry(PARAMFrame, textvariable=m2var, width=6, state="normal")
mdiff.entry <- tkentry(PARAMFrame, textvariable=mdiffvar, width=6, state="normal")
ppmerr.entry <- tkentry(PARAMFrame, textvariable=ppmerrvar, width=6, state="normal")
val.entry <- tkentry(PARAMFrame, textvariable=valvar, width=10, state="normal")
mdiff2.entry <- tkentry(PARAMFrame, textvariable=mdiff2var, width=6, state="normal")
myfile.entry <- tkentry(PARAMFrame, textvariable=myfilevar, width=25, state="normal")
myfile2.entry <- tkentry(PARAMFrame, textvariable=myfile2var, width=25, state="normal")
m1need.entry <- tkentry(PARAMFrame, textvariable=m1needvar, width=6, state="normal")
tkgrid(tklabel(PARAMFrame,text="xsAnnotate object : "), xsAnnotate.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="m1 : "),m1.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="m2 : "),m2.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="Thresh : "), Thresh.entry, sticky="w")
#tkgrid(tklabel(PARAMFrame,text="clppmerr: "),clppmerr.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text=" - OPTIONNAL Advanced cldetect Parameters -", foreground="blue"), columnspan=8)
tkgrid(tklabel(PARAMFrame,text="plotps : "), plotps.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="mdiff: "), mdiff.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="ppmerr: "),ppmerr.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="m1need: "),m1need.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="val : "), val.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="mdiff2: "), mdiff2.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="myfile: "),myfile.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="myfile2: "),myfile2.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="deprof: "),deprof.entry, sticky="w")
tkgrid(PARAMFrame, sticky="we")
#
# Local variables
#
done <- tclVar(0) # To terminate the dialog
################################
# Function to reset all dialog elements to default values
################################
"reset" <- function()
{
tclvalue(outdirvar)<-tclVar(as.character(getwd()))
tclvalue(matclvar)<-"matcl"
tclvalue(xsAnnotatevar)<-"an"
tclvalue(plotpsvar)<-"TRUE"
tclvalue(deprofvar)<-"FALSE"
# tclvalue(clppmerrvar)<-50
tclvalue(Threshvar)<-20
tclvalue(m1var)<-1.003
tclvalue(m2var)<-1.997
tclvalue(mdiffvar)<-0.05
tclvalue(ppmerrvar)<-50
tclvalue(valvar)<-"maxo"
tclvalue(mdiff2var)<-0.001
tclvalue(myfilevar)<-"halo_list.csv"
tclvalue(myfile2var)<-"halo_list_short.csv"
tclvalue(m1needvar)<-"FALSE"
}
################################
# Function to launch computations
################################
"execcomp" <- function()
{
outdir<-as.character(tclvalue(outdirvar))
if (outdir=="" ||is.null(outdir)==TRUE){
outdir<-tclvalue(tkchooseDirectory(title="Choose your Results folder"))
}
print("Processing...")
Sys.sleep(0.5)
tkdestroy(tt)
#test if xsAnnotate object exists in MeHaloCoAenv or .GlobalEnv
if(length(which(ls(MeHaloCoAenv)==tclvalue(xsAnnotatevar)))==0){
an<-get(ls(.GlobalEnv)[which(ls(.GlobalEnv)==tclvalue(xsAnnotatevar))], envir=as.environment(.GlobalEnv))
print("Note: Use of an xsAnnotate object from GlobalEnv as entry")
}else
{
an<-get(ls(MeHaloCoAenv)[which(ls(MeHaloCoAenv)==tclvalue(xsAnnotatevar))], envir=as.environment(MeHaloCoAenv))
}
if((class(an)=="xsAnnotate")==FALSE){
xsAnnotate<-an[as.vector(which(lapply(an,function(x)class(x))=="xsAnnotate"))]
}else
{
xsAnnotate<-an
}
print(xsAnnotate)
if (length(xsAnnotate)>1){
print("several files")
assign("matcl",vector(mode="list", length=length(xsAnnotate)), envir=as.environment(MeHaloCoAenv))
#projectpdf is a function that avoid overwriting IFC.pdf
projectpdf(dir=outdir,projectName="IFC", ext="pdf")
# pdf(file=file.path(outdir,"IFC%03d.pdf"))
mat<-list()
for (i in 1:length(xsAnnotate)){
MeHaloCoAenv$matcl[[i]]<<-do.call(cldetect,c(outdir=outdir,xsAnnotate=xsAnnotate[[i]],list(
plotps=tclvalue(plotpsvar),
deprof=tclvalue(deprofvar),
# clppmerr=as.numeric(tclvalue(clppmerrvar)),
Thresh=as.numeric(tclvalue(Threshvar)),
m1=as.numeric(tclvalue(m1var)),
m2=as.numeric(tclvalue(m2var)),
mdiff=as.numeric(tclvalue(mdiffvar)),
ppmerr=as.numeric(tclvalue(ppmerrvar)),
val=tclvalue(valvar),
mdiff2=as.numeric(tclvalue(mdiff2var)),
myfile=paste("file_",i,"_",tclvalue(myfilevar)),
myfile2=tclvalue(myfile2var),
m1need=tclvalue(m1needvar)
)
))
}
dev.off()
for (i in 1:length(MeHaloCoAenv$matcl)){
MeHaloCoAenv$matcl[[i]]<<-cbind(basename(xsAnnotate[[i]]@xcmsSet@filepaths),MeHaloCoAenv$matcl[[i]])
MeHaloCoAenv$matcl[[i]] <<- data.frame(lapply(MeHaloCoAenv$matcl[[i]], as.character), stringsAsFactors=FALSE)
colnames(MeHaloCoAenv$matcl[[i]])[1]<<-"File"
}
mat<-do.call("rbind",MeHaloCoAenv$matcl)
write.table(mat, file=file.path(outdir, tclvalue(myfile2var)), row.names=FALSE, sep="\t")
}
else{
projectpdf(dir=outdir,projectName="IFC", ext="pdf")
# pdf(file=file.path(outdir,"IFC%03d.pdf"))
assign(tclvalue(matclvar), do.call(cldetect,c(outdir=outdir,xsAnnotate=xsAnnotate,list(
plotps=tclvalue(plotpsvar),
deprof=tclvalue(deprofvar),
# clppmerr=as.numeric(tclvalue(clppmerrvar)),
Thresh=as.numeric(tclvalue(Threshvar)),
m1=as.numeric(tclvalue(m1var)),
m2=as.numeric(tclvalue(m2var)),
mdiff=as.numeric(tclvalue(mdiffvar)),
ppmerr=as.numeric(tclvalue(ppmerrvar)),
val=tclvalue(valvar),
mdiff2=as.numeric(tclvalue(mdiff2var)),
myfile=tclvalue(myfilevar),
myfile2=tclvalue(myfile2var),
m1need=tclvalue(m1needvar)
)
)), envir=as.environment(MeHaloCoAenv))
dev.off()
}
tkmessageBox(title="Done",message= "cldetect Step is Done",icon="info",type="ok")
}
#
# Reset Cancel and Submit buttons
#
RCSFrame <- tkframe(tt, relief="groove")
reset.but <- tkbutton(RCSFrame, text="Reset", command=reset)
cancel.but <- tkbutton(RCSFrame, text="Cancel", command=function() tkdestroy(tt))
submit.but <- tkbutton(RCSFrame, text="Submit", default="active", command=function() execcomp())
tkgrid(cancel.but, submit.but, reset.but, ipadx=20)
tkgrid(RCSFrame)
#
# If window is closed by user, terminate the dialog
#
tkbind(tt, "<Destroy>", function() tclvalue(done)<-2)
tkbind(tt, "<KeyPress-Return>", function() execcomp())
tkbind(tt, "<KeyPress-Escape>", function() tkdestroy(tt))
HELPFrame <- tkframe(tt, relief="groove", borderwidth=2)
tkgrid(tklabel(HELPFrame,text="- cldetect help -" , foreground="blue"),columnspan=2, sticky="we")
tkgrid(tklabel(HELPFrame,text="outdir: your results directory " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="xsAnnotate: an R CAMERA object created by CDF2Data.R function or xs<-xcmsSet() then an<-annotate(xs) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="plotps: Draw nice Isotopic Filtered Chromatogram (IFC) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="deprof: default=FALSE if TRUE deprofile.scan from RMassBank is applied on each pspectra" ),columnspan=2, sticky="w")
#tkgrid(tklabel(HELPFrame,text="clppmerr: error on M, M+1 or M+2 isotopes " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="Thresh: threshold of intensity for M+2 here 30 " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="m1: mass defect between M and M+1 isotope (here 1.0033) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="m2: mass defect between M and M+2 isotope (here 1.997 for Cl) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="mdiff: mdiff differences in Da applied to neutral loss search" ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="ppmerr: ppm margin tolerated by cldetect " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="m1need: Should M+1 isotope be present? if FALSE peaks with no M+1 are considered (interesting for low intensity compounds) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="val: can be into or maxo, area or intensity respectively " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="mdiff2: mdiff2 differences in Da applied to IFC chromatogram drawing " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="myfile: name of the output file default halo_list.csv" ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="myfile2: name of the output file default halo_list_short.csv is a resume from all individual myfile\n in the case off several files have been processed " ),columnspan=2, sticky="w")
tkgrid(HELPFrame, sticky="we")
#
# User closed the window
#
if(tclvalue(done)=="2") return()
}
if(method=="scan"){
#
# Main dialog window with title
#
tt <- tktoplevel()
tkwm.title(tt,"MeHaloCoA")
#
# Variables for text fields
#
outdirvar <- tclVar(as.character(getwd()))
indirvar <- tclVar(as.character(system.file("doc/mzData", package="MeHaloCoA"))) #
matclvar<-tclVar("matcl")
#
# Variable for number fields
#
# xsAnnotatevar<-tclVar("an")
plotpsvar<-tclVar("TRUE")
deprofvar<-tclVar("FALSE")
noisevar<-tclVar(500)
Nvar<-tclVar(5)
Threshvar<-tclVar(20)
m1var<-tclVar(1.003)
m2var<-tclVar(1.997)
mdiffvar<-tclVar(0.05)
ppmerrvar<-tclVar(50)
# valvar<-tclVar("maxo")
mdiff2var<-tclVar(0.001)
myfilevar<-tclVar("halo_list.csv")
myfile2var<-tclVar("halo_list_short.csv")
m1needvar<-tclVar("FALSE")
#
# Title
#
TFrame <- tkframe(tt, relief="groove")
labh <- tklabel(TFrame, bitmap="questhead")
tkgrid(tklabel(TFrame,text="cldetect.scan", font="Times 18", foreground="red"), labh)
tkbind(labh, "<Button-1>", function() print(help("cldetect.scan")))
tkgrid(TFrame)
#
# In and Out directories (option = files paths)
#
IOFrame <- tkframe(tt, relief="groove", borderwidth=2)
tkgrid(tklabel(IOFrame,text=" - Input & Output files -", foreground="blue"), columnspan=8)
indir.entry <- tkentry(IOFrame, textvariable=indirvar, width=55)
outdir.entry <- tkentry(IOFrame, textvariable=outdirvar, width=55)
"delinsert"<-function(arg,title1){
tkdelete(arg, 0, "end")
tkinsert(arg, "end", tclvalue(tkchooseDirectory(initialdir=getwd(),title=title1)))
}
choosedir.but <- tkbutton(IOFrame, text="Browse",command=function() delinsert(arg=indir.entry, title1="Your Data Directory"))
choosedir.but2 <- tkbutton(IOFrame, text="Browse",command=function() delinsert(arg=outdir.entry, title1="Your Result Directory"))
tkgrid(tklabel(IOFrame,text="Data path (indir) : "), indir.entry,choosedir.but, tklabel(IOFrame,text=" Path to your Data") , sticky="w")
tkgrid(tklabel(IOFrame,text="Output path (outdir) : "), outdir.entry,choosedir.but2,tklabel(IOFrame,text="Path for Results "), sticky="w")
tkgrid(IOFrame, sticky="we")
#settings list for halogen detection algorithm
# "xsAnnotate" "plotps" "deprof" "clppmerr" "Thresh" "m1" "m2" "mdiff" "ppmerr"
# "val" "mdiff2" "myfile" "myfile2"
PARAMFrame <- tkframe(tt, relief="groove", borderwidth=2)
tkgrid(tklabel(PARAMFrame,text=" - cldetect.scan Parameters -", foreground="blue"), columnspan=8)
# xsAnnotate.entry <- tkentry(PARAMFrame, textvariable=xsAnnotatevar, width=6, state="normal")
# plotps.entry <- tkentry(PARAMFrame, textvariable=plotpsvar, width=6, state="normal")
deprof.entry <- tkentry(PARAMFrame, textvariable=deprofvar, width=6, state="normal")
noise.entry <- tkentry(PARAMFrame, textvariable=noisevar, width=6, state="normal")
N.entry <- tkentry(PARAMFrame, textvariable=Nvar, width=6, state="normal")
Thresh.entry <- tkentry(PARAMFrame, textvariable=Threshvar, width=6, state="normal")
m1.entry <- tkentry(PARAMFrame, textvariable=m1var, width=6, state="normal")
m2.entry <- tkentry(PARAMFrame, textvariable=m2var, width=6, state="normal")
mdiff.entry <- tkentry(PARAMFrame, textvariable=mdiffvar, width=6, state="normal")
ppmerr.entry <- tkentry(PARAMFrame, textvariable=ppmerrvar, width=6, state="normal")
# val.entry <- tkentry(PARAMFrame, textvariable=valvar, width=10, state="normal")
mdiff2.entry <- tkentry(PARAMFrame, textvariable=mdiff2var, width=6, state="normal")
myfile.entry <- tkentry(PARAMFrame, textvariable=myfilevar, width=25, state="normal")
myfile2.entry <- tkentry(PARAMFrame, textvariable=myfile2var, width=25, state="normal")
m1need.entry <- tkentry(PARAMFrame, textvariable=m1needvar, width=6, state="normal")
# tkgrid(tklabel(PARAMFrame,text="xsAnnotate object : "), xsAnnotate.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="m1 : "),m1.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="m2 : "),m2.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="Thresh : "), Thresh.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="noise: "),noise.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="N: "),N.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text=" - OPTIONNAL Advanced cldetect.scan Parameters -", foreground="blue"), columnspan=8)
# tkgrid(tklabel(PARAMFrame,text="plotps : "), plotps.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="mdiff: "), mdiff.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="ppmerr: "),ppmerr.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="m1need: "),m1need.entry, sticky="w")
# tkgrid(tklabel(PARAMFrame,text="val : "), val.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="mdiff2: "), mdiff2.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="myfile: "),myfile.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="myfile2: "),myfile2.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="deprof: "),deprof.entry, sticky="w")
tkgrid(PARAMFrame, sticky="we")
#
# Local variables
#
done <- tclVar(0) # To terminate the dialog
################################
# Function to reset all dialog elements to default values
################################
"reset" <- function()
{
tclvalue(indirvar)<-tclVar(as.character(getwd()))
tclvalue(outdirvar)<-tclVar(as.character(getwd()))
tclvalue(matclvar)<-"matcl"
# tclvalue(xsAnnotatevar)<-"an"
# tclvalue(plotpsvar)<-"TRUE"
tclvalue(deprofvar)<-"FALSE"
tclvalue(noisevar)<-500
tclvalue(Nvar)<-5
tclvalue(Threshvar)<-20
tclvalue(m1var)<-1.003
tclvalue(m2var)<-1.997
tclvalue(mdiffvar)<-0.05
tclvalue(ppmerrvar)<-50
# tclvalue(valvar)<-"maxo"
tclvalue(mdiff2var)<-0.001
tclvalue(myfilevar)<-"halo_list.csv"
tclvalue(myfile2var)<-"halo_list_short.csv"
tclvalue(m1needvar)<-"FALSE"
}
################################
# Function to launch computations
################################
"execcomp" <- function()
{
outdir<-as.character(tclvalue(outdirvar))
if (outdir=="" ||is.null(outdir)==TRUE){
outdir<-tclvalue(tkchooseDirectory(title="Choose your Results folder"))
}
indir<-tclvalue(indirvar)
print("Processing...")
Sys.sleep(0.5)
tkdestroy(tt)
#test if xsAnnotate object exists in MeHaloCoAenv or .GlobalEnv
# if(length(which(ls(MeHaloCoAenv)==tclvalue(xsAnnotatevar)))==0){
# an<-get(ls(.GlobalEnv)[which(ls(.GlobalEnv)==tclvalue(xsAnnotatevar))], envir=as.environment(.GlobalEnv))
# print("Note: Use of an xsAnnotate object from GlobalEnv as entry")
# }else
# {
# an<-get(ls(MeHaloCoAenv)[which(ls(MeHaloCoAenv)==tclvalue(xsAnnotatevar))], envir=as.environment(MeHaloCoAenv))
# }
# if((class(an)=="xsAnnotate")==FALSE){
# xsAnnotate<-an[as.vector(which(lapply(an,function(x)class(x))=="xsAnnotate"))]
# }else
# {
# xsAnnotate<-an
# }
# print(xsAnnotate)
filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
samples<-list.files(path=tclvalue(indirvar), pattern=filepattern, all.files=FALSE,recursive=TRUE,full.names=TRUE,ignore.case=FALSE)
if (length(samples)>1){
print("several files")
assign("matcl",vector(mode="list", length=length(samples)), envir=as.environment(MeHaloCoAenv))
projectpdf(dir=outdir,projectName="IFC", ext="pdf")
mat<-list()
for (i in 1:length(samples)){
#debugg
print(paste("sample:",sample[i]))
# scanrange=NULL
MeHaloCoAenv$matcl[[i]]<<-do.call(cldetect.scan,c(outdir=outdir,file=samples[[i]],list(
# plotps=tclvalue(plotpsvar),
deprof=tclvalue(deprofvar),
noise=as.numeric(tclvalue(noisevar)),
N=as.numeric(tclvalue(Nvar)),
Thresh=as.numeric(tclvalue(Threshvar)),
m1=as.numeric(tclvalue(m1var)),
m2=as.numeric(tclvalue(m2var)),
mdiff=as.numeric(tclvalue(mdiffvar)),
ppmerr=as.numeric(tclvalue(ppmerrvar)),
mdiff2=as.numeric(tclvalue(mdiff2var)),
myfile=paste("file_",i,"_",tclvalue(myfilevar)),
myfile2=tclvalue(myfile2var),
m1need=tclvalue(m1needvar)
)
))
}
dev.off()
for (i in 1:length(MeHaloCoAenv$matcl)){
MeHaloCoAenv$matcl[[i]]<<-cbind(basename(samples[[i]]),MeHaloCoAenv$matcl[[i]])
MeHaloCoAenv$matcl[[i]] <<- data.frame(lapply(MeHaloCoAenv$matcl[[i]], as.character), stringsAsFactors=FALSE)
colnames(MeHaloCoAenv$matcl[[i]])[1]<<-"File"
}
mat<-do.call("rbind",MeHaloCoAenv$matcl)
write.table(mat, file=file.path(outdir, tclvalue(myfile2var)), row.names=FALSE, sep="\t")
}
else{
projectpdf(dir=outdir,projectName="IFC", ext="pdf")
assign(tclvalue(matclvar), do.call(cldetect.scan,c(outdir=outdir,file=samples[[1]],list(
# plotps=tclvalue(plotpsvar),
deprof=tclvalue(deprofvar),
noise=as.numeric(tclvalue(noisevar)),
N=as.numeric(tclvalue(Nvar)),
Thresh=as.numeric(tclvalue(Threshvar)),
m1=as.numeric(tclvalue(m1var)),
m2=as.numeric(tclvalue(m2var)),
mdiff=as.numeric(tclvalue(mdiffvar)),
ppmerr=as.numeric(tclvalue(ppmerrvar)),
# val=tclvalue(valvar),
mdiff2=as.numeric(tclvalue(mdiff2var)),
myfile=tclvalue(myfilevar),
myfile2=tclvalue(myfile2var),
m1need=tclvalue(m1needvar)
)
)), envir=as.environment(MeHaloCoAenv))
dev.off()
}
tkmessageBox(title="Done",message= "cldetect Step is Done",icon="info",type="ok")
}
#
# Reset Cancel and Submit buttons
#
RCSFrame <- tkframe(tt, relief="groove")
reset.but <- tkbutton(RCSFrame, text="Reset", command=reset)
cancel.but <- tkbutton(RCSFrame, text="Cancel", command=function() tkdestroy(tt))
submit.but <- tkbutton(RCSFrame, text="Submit", default="active", command=function() execcomp())
tkgrid(cancel.but, submit.but, reset.but, ipadx=20)
tkgrid(RCSFrame)
#
# If window is closed by user, terminate the dialog
#
tkbind(tt, "<Destroy>", function() tclvalue(done)<-2)
tkbind(tt, "<KeyPress-Return>", function() execcomp())
tkbind(tt, "<KeyPress-Escape>", function() tkdestroy(tt))
HELPFrame <- tkframe(tt, relief="groove", borderwidth=2)
tkgrid(tklabel(HELPFrame,text="- cldetect help -" , foreground="blue"),columnspan=2, sticky="we")
tkgrid(tklabel(HELPFrame,text="indir: your Data directory " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="outdir: your results directory " ),columnspan=2, sticky="w")
# tkgrid(tklabel(HELPFrame,text="plotps: Draw nice Isotopic Filtered Chromatogram (IFC) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="deprof: default=FALSE if TRUE deprofile.scan from RMassBank is applied on each pspectra" ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="noise: noise level below which scan are no taken " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="N: number of scan merged before calculation N/2 scan before target + N/2 scan after " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="Thresh: threshold of intensity for M+2 here 30 " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="m1: mass defect between M and M+1 isotope (here 1.0033) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="m2: mass defect between M and M+2 isotope (here 1.997 for Cl) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="mdiff: mdiff differences in Da applied to neutral loss search" ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="ppmerr: ppm margin tolerated by cldetect " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="m1need: Should M+1 isotope be present? if FALSE peaks with no M+1 are considered (interesting for low intensity compounds) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="val: can be into or maxo, area or intensity respectively " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="mdiff2: mdiff2 differences in Da applied to IFC chromatogram drawing " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="myfile: name of the output file default halo_list.csv" ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="myfile2: name of the output file default halo_list_short.csv is a resume from all individual myfile\n in the case off several files have been processed " ),columnspan=2, sticky="w")
tkgrid(HELPFrame, sticky="we")
#
# User closed the window
#
if(tclvalue(done)=="2") return()
}
}
yguitton/MeHaloCoA documentation built on May 3, 2019, 4:30 p.m.
R Package Documentation
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# MeHaloCoA Tcl/Tk GUI for halogeneted compound search in MS data.
# Part of the code is based on the ade4TkGUI package by Jean Thioulouse <jthioulouse@biomserv.univ-lyon1.fr>, Stephane
# Dray <dray@biomserv.univ-lyon1.fr>
#cldetect function dialog frame
dialog.mehalocoa.cldetect <-
function(method="")
{
if(method==""){
#
# Main dialog window with title
#
tt <- tktoplevel()
tkwm.title(tt,"MeHaloCoA")
#
# Variables for text fields
#
outdirvar <- tclVar(as.character(getwd()))
matclvar<-tclVar("matcl")
#
# Variable for number fields
#
xsAnnotatevar<-tclVar("an")
plotpsvar<-tclVar("TRUE")
deprofvar<-tclVar("FALSE")
#clppmerrvar<-tclVar(50)
Threshvar<-tclVar(20)
m1var<-tclVar(1.003)
m2var<-tclVar(1.997)
mdiffvar<-tclVar(0.05)
ppmerrvar<-tclVar(50)
valvar<-tclVar("maxo")
mdiff2var<-tclVar(0.001)
myfilevar<-tclVar("halo_list.csv")
myfile2var<-tclVar("halo_list_short.csv")
m1needvar<-tclVar("FALSE")
#
# Title
#
TFrame <- tkframe(tt, relief="groove")
labh <- tklabel(TFrame, bitmap="questhead")
tkgrid(tklabel(TFrame,text="MeHaloCoA::cldetect", font="Times 18", foreground="red"), labh)
tkbind(labh, "<Button-1>", function() print(help("cldetect")))
tkgrid(TFrame)
#
# In and Out directories (option = files paths)
#
IOFrame <- tkframe(tt, relief="groove", borderwidth=2)
tkgrid(tklabel(IOFrame,text=" - Input & Output files -", foreground="blue"), columnspan=8)
outdir.entry <- tkentry(IOFrame, textvariable=outdirvar, width=55)
"delinsert"<-function(arg,title1){
tkdelete(arg, 0, "end")
tkinsert(arg, "end", tclvalue(tkchooseDirectory(initialdir=getwd(),title=title1)))
}
choosedir.but2 <- tkbutton(IOFrame, text="Browse",command=function() delinsert(arg=outdir.entry, title1="Your Result Directory"))
tkgrid(tklabel(IOFrame,text="Output path (outdir) : "), outdir.entry,choosedir.but2,tklabel(IOFrame,text="Path for Results "), sticky="w")
tkgrid(IOFrame, sticky="we")
#settings list for halogen detection algorithm
# "xsAnnotate" "plotps" "deprof" "clppmerr" "Thresh" "m1" "m2" "mdiff" "ppmerr"
# "val" "mdiff2" "myfile" "myfile2"
PARAMFrame <- tkframe(tt, relief="groove", borderwidth=2)
tkgrid(tklabel(PARAMFrame,text=" - cldetect Parameters -", foreground="blue"), columnspan=8)
xsAnnotate.entry <- tkentry(PARAMFrame, textvariable=xsAnnotatevar, width=6, state="normal")
plotps.entry <- tkentry(PARAMFrame, textvariable=plotpsvar, width=6, state="normal")
deprof.entry <- tkentry(PARAMFrame, textvariable=deprofvar, width=6, state="normal")
#clppmerr.entry <- tkentry(PARAMFrame, textvariable=clppmerrvar, width=6, state="normal")
Thresh.entry <- tkentry(PARAMFrame, textvariable=Threshvar, width=6, state="normal")
m1.entry <- tkentry(PARAMFrame, textvariable=m1var, width=6, state="normal")
m2.entry <- tkentry(PARAMFrame, textvariable=m2var, width=6, state="normal")
mdiff.entry <- tkentry(PARAMFrame, textvariable=mdiffvar, width=6, state="normal")
ppmerr.entry <- tkentry(PARAMFrame, textvariable=ppmerrvar, width=6, state="normal")
val.entry <- tkentry(PARAMFrame, textvariable=valvar, width=10, state="normal")
mdiff2.entry <- tkentry(PARAMFrame, textvariable=mdiff2var, width=6, state="normal")
myfile.entry <- tkentry(PARAMFrame, textvariable=myfilevar, width=25, state="normal")
myfile2.entry <- tkentry(PARAMFrame, textvariable=myfile2var, width=25, state="normal")
m1need.entry <- tkentry(PARAMFrame, textvariable=m1needvar, width=6, state="normal")
tkgrid(tklabel(PARAMFrame,text="xsAnnotate object : "), xsAnnotate.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="m1 : "),m1.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="m2 : "),m2.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="Thresh : "), Thresh.entry, sticky="w")
#tkgrid(tklabel(PARAMFrame,text="clppmerr: "),clppmerr.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text=" - OPTIONNAL Advanced cldetect Parameters -", foreground="blue"), columnspan=8)
tkgrid(tklabel(PARAMFrame,text="plotps : "), plotps.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="mdiff: "), mdiff.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="ppmerr: "),ppmerr.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="m1need: "),m1need.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="val : "), val.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="mdiff2: "), mdiff2.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="myfile: "),myfile.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="myfile2: "),myfile2.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="deprof: "),deprof.entry, sticky="w")
tkgrid(PARAMFrame, sticky="we")
#
# Local variables
#
done <- tclVar(0) # To terminate the dialog
################################
# Function to reset all dialog elements to default values
################################
"reset" <- function()
{
tclvalue(outdirvar)<-tclVar(as.character(getwd()))
tclvalue(matclvar)<-"matcl"
tclvalue(xsAnnotatevar)<-"an"
tclvalue(plotpsvar)<-"TRUE"
tclvalue(deprofvar)<-"FALSE"
# tclvalue(clppmerrvar)<-50
tclvalue(Threshvar)<-20
tclvalue(m1var)<-1.003
tclvalue(m2var)<-1.997
tclvalue(mdiffvar)<-0.05
tclvalue(ppmerrvar)<-50
tclvalue(valvar)<-"maxo"
tclvalue(mdiff2var)<-0.001
tclvalue(myfilevar)<-"halo_list.csv"
tclvalue(myfile2var)<-"halo_list_short.csv"
tclvalue(m1needvar)<-"FALSE"
}
################################
# Function to launch computations
################################
"execcomp" <- function()
{
outdir<-as.character(tclvalue(outdirvar))
if (outdir=="" ||is.null(outdir)==TRUE){
outdir<-tclvalue(tkchooseDirectory(title="Choose your Results folder"))
}
print("Processing...")
Sys.sleep(0.5)
tkdestroy(tt)
#test if xsAnnotate object exists in MeHaloCoAenv or .GlobalEnv
if(length(which(ls(MeHaloCoAenv)==tclvalue(xsAnnotatevar)))==0){
an<-get(ls(.GlobalEnv)[which(ls(.GlobalEnv)==tclvalue(xsAnnotatevar))], envir=as.environment(.GlobalEnv))
print("Note: Use of an xsAnnotate object from GlobalEnv as entry")
}else
{
an<-get(ls(MeHaloCoAenv)[which(ls(MeHaloCoAenv)==tclvalue(xsAnnotatevar))], envir=as.environment(MeHaloCoAenv))
}
if((class(an)=="xsAnnotate")==FALSE){
xsAnnotate<-an[as.vector(which(lapply(an,function(x)class(x))=="xsAnnotate"))]
}else
{
xsAnnotate<-an
}
print(xsAnnotate)
if (length(xsAnnotate)>1){
print("several files")
assign("matcl",vector(mode="list", length=length(xsAnnotate)), envir=as.environment(MeHaloCoAenv))
#projectpdf is a function that avoid overwriting IFC.pdf
projectpdf(dir=outdir,projectName="IFC", ext="pdf")
# pdf(file=file.path(outdir,"IFC%03d.pdf"))
mat<-list()
for (i in 1:length(xsAnnotate)){
MeHaloCoAenv$matcl[[i]]<<-do.call(cldetect,c(outdir=outdir,xsAnnotate=xsAnnotate[[i]],list(
plotps=tclvalue(plotpsvar),
deprof=tclvalue(deprofvar),
# clppmerr=as.numeric(tclvalue(clppmerrvar)),
Thresh=as.numeric(tclvalue(Threshvar)),
m1=as.numeric(tclvalue(m1var)),
m2=as.numeric(tclvalue(m2var)),
mdiff=as.numeric(tclvalue(mdiffvar)),
ppmerr=as.numeric(tclvalue(ppmerrvar)),
val=tclvalue(valvar),
mdiff2=as.numeric(tclvalue(mdiff2var)),
myfile=paste("file_",i,"_",tclvalue(myfilevar)),
myfile2=tclvalue(myfile2var),
m1need=tclvalue(m1needvar)
)
))
}
dev.off()
for (i in 1:length(MeHaloCoAenv$matcl)){
MeHaloCoAenv$matcl[[i]]<<-cbind(basename(xsAnnotate[[i]]@xcmsSet@filepaths),MeHaloCoAenv$matcl[[i]])
MeHaloCoAenv$matcl[[i]] <<- data.frame(lapply(MeHaloCoAenv$matcl[[i]], as.character), stringsAsFactors=FALSE)
colnames(MeHaloCoAenv$matcl[[i]])[1]<<-"File"
}
mat<-do.call("rbind",MeHaloCoAenv$matcl)
write.table(mat, file=file.path(outdir, tclvalue(myfile2var)), row.names=FALSE, sep="\t")
}
else{
projectpdf(dir=outdir,projectName="IFC", ext="pdf")
# pdf(file=file.path(outdir,"IFC%03d.pdf"))
assign(tclvalue(matclvar), do.call(cldetect,c(outdir=outdir,xsAnnotate=xsAnnotate,list(
plotps=tclvalue(plotpsvar),
deprof=tclvalue(deprofvar),
# clppmerr=as.numeric(tclvalue(clppmerrvar)),
Thresh=as.numeric(tclvalue(Threshvar)),
m1=as.numeric(tclvalue(m1var)),
m2=as.numeric(tclvalue(m2var)),
mdiff=as.numeric(tclvalue(mdiffvar)),
ppmerr=as.numeric(tclvalue(ppmerrvar)),
val=tclvalue(valvar),
mdiff2=as.numeric(tclvalue(mdiff2var)),
myfile=tclvalue(myfilevar),
myfile2=tclvalue(myfile2var),
m1need=tclvalue(m1needvar)
)
)), envir=as.environment(MeHaloCoAenv))
dev.off()
}
tkmessageBox(title="Done",message= "cldetect Step is Done",icon="info",type="ok")
}
#
# Reset Cancel and Submit buttons
#
RCSFrame <- tkframe(tt, relief="groove")
reset.but <- tkbutton(RCSFrame, text="Reset", command=reset)
cancel.but <- tkbutton(RCSFrame, text="Cancel", command=function() tkdestroy(tt))
submit.but <- tkbutton(RCSFrame, text="Submit", default="active", command=function() execcomp())
tkgrid(cancel.but, submit.but, reset.but, ipadx=20)
tkgrid(RCSFrame)
#
# If window is closed by user, terminate the dialog
#
tkbind(tt, "<Destroy>", function() tclvalue(done)<-2)
tkbind(tt, "<KeyPress-Return>", function() execcomp())
tkbind(tt, "<KeyPress-Escape>", function() tkdestroy(tt))
HELPFrame <- tkframe(tt, relief="groove", borderwidth=2)
tkgrid(tklabel(HELPFrame,text="- cldetect help -" , foreground="blue"),columnspan=2, sticky="we")
tkgrid(tklabel(HELPFrame,text="outdir: your results directory " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="xsAnnotate: an R CAMERA object created by CDF2Data.R function or xs<-xcmsSet() then an<-annotate(xs) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="plotps: Draw nice Isotopic Filtered Chromatogram (IFC) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="deprof: default=FALSE if TRUE deprofile.scan from RMassBank is applied on each pspectra" ),columnspan=2, sticky="w")
#tkgrid(tklabel(HELPFrame,text="clppmerr: error on M, M+1 or M+2 isotopes " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="Thresh: threshold of intensity for M+2 here 30 " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="m1: mass defect between M and M+1 isotope (here 1.0033) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="m2: mass defect between M and M+2 isotope (here 1.997 for Cl) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="mdiff: mdiff differences in Da applied to neutral loss search" ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="ppmerr: ppm margin tolerated by cldetect " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="m1need: Should M+1 isotope be present? if FALSE peaks with no M+1 are considered (interesting for low intensity compounds) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="val: can be into or maxo, area or intensity respectively " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="mdiff2: mdiff2 differences in Da applied to IFC chromatogram drawing " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="myfile: name of the output file default halo_list.csv" ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="myfile2: name of the output file default halo_list_short.csv is a resume from all individual myfile\n in the case off several files have been processed " ),columnspan=2, sticky="w")
tkgrid(HELPFrame, sticky="we")
#
# User closed the window
#
if(tclvalue(done)=="2") return()
}
if(method=="scan"){
#
# Main dialog window with title
#
tt <- tktoplevel()
tkwm.title(tt,"MeHaloCoA")
#
# Variables for text fields
#
outdirvar <- tclVar(as.character(getwd()))
indirvar <- tclVar(as.character(system.file("doc/mzData", package="MeHaloCoA"))) #
matclvar<-tclVar("matcl")
#
# Variable for number fields
#
# xsAnnotatevar<-tclVar("an")
plotpsvar<-tclVar("TRUE")
deprofvar<-tclVar("FALSE")
noisevar<-tclVar(500)
Nvar<-tclVar(5)
Threshvar<-tclVar(20)
m1var<-tclVar(1.003)
m2var<-tclVar(1.997)
mdiffvar<-tclVar(0.05)
ppmerrvar<-tclVar(50)
# valvar<-tclVar("maxo")
mdiff2var<-tclVar(0.001)
myfilevar<-tclVar("halo_list.csv")
myfile2var<-tclVar("halo_list_short.csv")
m1needvar<-tclVar("FALSE")
#
# Title
#
TFrame <- tkframe(tt, relief="groove")
labh <- tklabel(TFrame, bitmap="questhead")
tkgrid(tklabel(TFrame,text="cldetect.scan", font="Times 18", foreground="red"), labh)
tkbind(labh, "<Button-1>", function() print(help("cldetect.scan")))
tkgrid(TFrame)
#
# In and Out directories (option = files paths)
#
IOFrame <- tkframe(tt, relief="groove", borderwidth=2)
tkgrid(tklabel(IOFrame,text=" - Input & Output files -", foreground="blue"), columnspan=8)
indir.entry <- tkentry(IOFrame, textvariable=indirvar, width=55)
outdir.entry <- tkentry(IOFrame, textvariable=outdirvar, width=55)
"delinsert"<-function(arg,title1){
tkdelete(arg, 0, "end")
tkinsert(arg, "end", tclvalue(tkchooseDirectory(initialdir=getwd(),title=title1)))
}
choosedir.but <- tkbutton(IOFrame, text="Browse",command=function() delinsert(arg=indir.entry, title1="Your Data Directory"))
choosedir.but2 <- tkbutton(IOFrame, text="Browse",command=function() delinsert(arg=outdir.entry, title1="Your Result Directory"))
tkgrid(tklabel(IOFrame,text="Data path (indir) : "), indir.entry,choosedir.but, tklabel(IOFrame,text=" Path to your Data") , sticky="w")
tkgrid(tklabel(IOFrame,text="Output path (outdir) : "), outdir.entry,choosedir.but2,tklabel(IOFrame,text="Path for Results "), sticky="w")
tkgrid(IOFrame, sticky="we")
#settings list for halogen detection algorithm
# "xsAnnotate" "plotps" "deprof" "clppmerr" "Thresh" "m1" "m2" "mdiff" "ppmerr"
# "val" "mdiff2" "myfile" "myfile2"
PARAMFrame <- tkframe(tt, relief="groove", borderwidth=2)
tkgrid(tklabel(PARAMFrame,text=" - cldetect.scan Parameters -", foreground="blue"), columnspan=8)
# xsAnnotate.entry <- tkentry(PARAMFrame, textvariable=xsAnnotatevar, width=6, state="normal")
# plotps.entry <- tkentry(PARAMFrame, textvariable=plotpsvar, width=6, state="normal")
deprof.entry <- tkentry(PARAMFrame, textvariable=deprofvar, width=6, state="normal")
noise.entry <- tkentry(PARAMFrame, textvariable=noisevar, width=6, state="normal")
N.entry <- tkentry(PARAMFrame, textvariable=Nvar, width=6, state="normal")
Thresh.entry <- tkentry(PARAMFrame, textvariable=Threshvar, width=6, state="normal")
m1.entry <- tkentry(PARAMFrame, textvariable=m1var, width=6, state="normal")
m2.entry <- tkentry(PARAMFrame, textvariable=m2var, width=6, state="normal")
mdiff.entry <- tkentry(PARAMFrame, textvariable=mdiffvar, width=6, state="normal")
ppmerr.entry <- tkentry(PARAMFrame, textvariable=ppmerrvar, width=6, state="normal")
# val.entry <- tkentry(PARAMFrame, textvariable=valvar, width=10, state="normal")
mdiff2.entry <- tkentry(PARAMFrame, textvariable=mdiff2var, width=6, state="normal")
myfile.entry <- tkentry(PARAMFrame, textvariable=myfilevar, width=25, state="normal")
myfile2.entry <- tkentry(PARAMFrame, textvariable=myfile2var, width=25, state="normal")
m1need.entry <- tkentry(PARAMFrame, textvariable=m1needvar, width=6, state="normal")
# tkgrid(tklabel(PARAMFrame,text="xsAnnotate object : "), xsAnnotate.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="m1 : "),m1.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="m2 : "),m2.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="Thresh : "), Thresh.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="noise: "),noise.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="N: "),N.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text=" - OPTIONNAL Advanced cldetect.scan Parameters -", foreground="blue"), columnspan=8)
# tkgrid(tklabel(PARAMFrame,text="plotps : "), plotps.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="mdiff: "), mdiff.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="ppmerr: "),ppmerr.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="m1need: "),m1need.entry, sticky="w")
# tkgrid(tklabel(PARAMFrame,text="val : "), val.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="mdiff2: "), mdiff2.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="myfile: "),myfile.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="myfile2: "),myfile2.entry, sticky="w")
tkgrid(tklabel(PARAMFrame,text="deprof: "),deprof.entry, sticky="w")
tkgrid(PARAMFrame, sticky="we")
#
# Local variables
#
done <- tclVar(0) # To terminate the dialog
################################
# Function to reset all dialog elements to default values
################################
"reset" <- function()
{
tclvalue(indirvar)<-tclVar(as.character(getwd()))
tclvalue(outdirvar)<-tclVar(as.character(getwd()))
tclvalue(matclvar)<-"matcl"
# tclvalue(xsAnnotatevar)<-"an"
# tclvalue(plotpsvar)<-"TRUE"
tclvalue(deprofvar)<-"FALSE"
tclvalue(noisevar)<-500
tclvalue(Nvar)<-5
tclvalue(Threshvar)<-20
tclvalue(m1var)<-1.003
tclvalue(m2var)<-1.997
tclvalue(mdiffvar)<-0.05
tclvalue(ppmerrvar)<-50
# tclvalue(valvar)<-"maxo"
tclvalue(mdiff2var)<-0.001
tclvalue(myfilevar)<-"halo_list.csv"
tclvalue(myfile2var)<-"halo_list_short.csv"
tclvalue(m1needvar)<-"FALSE"
}
################################
# Function to launch computations
################################
"execcomp" <- function()
{
outdir<-as.character(tclvalue(outdirvar))
if (outdir=="" ||is.null(outdir)==TRUE){
outdir<-tclvalue(tkchooseDirectory(title="Choose your Results folder"))
}
indir<-tclvalue(indirvar)
print("Processing...")
Sys.sleep(0.5)
tkdestroy(tt)
#test if xsAnnotate object exists in MeHaloCoAenv or .GlobalEnv
# if(length(which(ls(MeHaloCoAenv)==tclvalue(xsAnnotatevar)))==0){
# an<-get(ls(.GlobalEnv)[which(ls(.GlobalEnv)==tclvalue(xsAnnotatevar))], envir=as.environment(.GlobalEnv))
# print("Note: Use of an xsAnnotate object from GlobalEnv as entry")
# }else
# {
# an<-get(ls(MeHaloCoAenv)[which(ls(MeHaloCoAenv)==tclvalue(xsAnnotatevar))], envir=as.environment(MeHaloCoAenv))
# }
# if((class(an)=="xsAnnotate")==FALSE){
# xsAnnotate<-an[as.vector(which(lapply(an,function(x)class(x))=="xsAnnotate"))]
# }else
# {
# xsAnnotate<-an
# }
# print(xsAnnotate)
filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
samples<-list.files(path=tclvalue(indirvar), pattern=filepattern, all.files=FALSE,recursive=TRUE,full.names=TRUE,ignore.case=FALSE)
if (length(samples)>1){
print("several files")
assign("matcl",vector(mode="list", length=length(samples)), envir=as.environment(MeHaloCoAenv))
projectpdf(dir=outdir,projectName="IFC", ext="pdf")
mat<-list()
for (i in 1:length(samples)){
#debugg
print(paste("sample:",sample[i]))
# scanrange=NULL
MeHaloCoAenv$matcl[[i]]<<-do.call(cldetect.scan,c(outdir=outdir,file=samples[[i]],list(
# plotps=tclvalue(plotpsvar),
deprof=tclvalue(deprofvar),
noise=as.numeric(tclvalue(noisevar)),
N=as.numeric(tclvalue(Nvar)),
Thresh=as.numeric(tclvalue(Threshvar)),
m1=as.numeric(tclvalue(m1var)),
m2=as.numeric(tclvalue(m2var)),
mdiff=as.numeric(tclvalue(mdiffvar)),
ppmerr=as.numeric(tclvalue(ppmerrvar)),
mdiff2=as.numeric(tclvalue(mdiff2var)),
myfile=paste("file_",i,"_",tclvalue(myfilevar)),
myfile2=tclvalue(myfile2var),
m1need=tclvalue(m1needvar)
)
))
}
dev.off()
for (i in 1:length(MeHaloCoAenv$matcl)){
MeHaloCoAenv$matcl[[i]]<<-cbind(basename(samples[[i]]),MeHaloCoAenv$matcl[[i]])
MeHaloCoAenv$matcl[[i]] <<- data.frame(lapply(MeHaloCoAenv$matcl[[i]], as.character), stringsAsFactors=FALSE)
colnames(MeHaloCoAenv$matcl[[i]])[1]<<-"File"
}
mat<-do.call("rbind",MeHaloCoAenv$matcl)
write.table(mat, file=file.path(outdir, tclvalue(myfile2var)), row.names=FALSE, sep="\t")
}
else{
projectpdf(dir=outdir,projectName="IFC", ext="pdf")
assign(tclvalue(matclvar), do.call(cldetect.scan,c(outdir=outdir,file=samples[[1]],list(
# plotps=tclvalue(plotpsvar),
deprof=tclvalue(deprofvar),
noise=as.numeric(tclvalue(noisevar)),
N=as.numeric(tclvalue(Nvar)),
Thresh=as.numeric(tclvalue(Threshvar)),
m1=as.numeric(tclvalue(m1var)),
m2=as.numeric(tclvalue(m2var)),
mdiff=as.numeric(tclvalue(mdiffvar)),
ppmerr=as.numeric(tclvalue(ppmerrvar)),
# val=tclvalue(valvar),
mdiff2=as.numeric(tclvalue(mdiff2var)),
myfile=tclvalue(myfilevar),
myfile2=tclvalue(myfile2var),
m1need=tclvalue(m1needvar)
)
)), envir=as.environment(MeHaloCoAenv))
dev.off()
}
tkmessageBox(title="Done",message= "cldetect Step is Done",icon="info",type="ok")
}
#
# Reset Cancel and Submit buttons
#
RCSFrame <- tkframe(tt, relief="groove")
reset.but <- tkbutton(RCSFrame, text="Reset", command=reset)
cancel.but <- tkbutton(RCSFrame, text="Cancel", command=function() tkdestroy(tt))
submit.but <- tkbutton(RCSFrame, text="Submit", default="active", command=function() execcomp())
tkgrid(cancel.but, submit.but, reset.but, ipadx=20)
tkgrid(RCSFrame)
#
# If window is closed by user, terminate the dialog
#
tkbind(tt, "<Destroy>", function() tclvalue(done)<-2)
tkbind(tt, "<KeyPress-Return>", function() execcomp())
tkbind(tt, "<KeyPress-Escape>", function() tkdestroy(tt))
HELPFrame <- tkframe(tt, relief="groove", borderwidth=2)
tkgrid(tklabel(HELPFrame,text="- cldetect help -" , foreground="blue"),columnspan=2, sticky="we")
tkgrid(tklabel(HELPFrame,text="indir: your Data directory " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="outdir: your results directory " ),columnspan=2, sticky="w")
# tkgrid(tklabel(HELPFrame,text="plotps: Draw nice Isotopic Filtered Chromatogram (IFC) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="deprof: default=FALSE if TRUE deprofile.scan from RMassBank is applied on each pspectra" ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="noise: noise level below which scan are no taken " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="N: number of scan merged before calculation N/2 scan before target + N/2 scan after " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="Thresh: threshold of intensity for M+2 here 30 " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="m1: mass defect between M and M+1 isotope (here 1.0033) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="m2: mass defect between M and M+2 isotope (here 1.997 for Cl) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="mdiff: mdiff differences in Da applied to neutral loss search" ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="ppmerr: ppm margin tolerated by cldetect " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="m1need: Should M+1 isotope be present? if FALSE peaks with no M+1 are considered (interesting for low intensity compounds) " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="val: can be into or maxo, area or intensity respectively " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="mdiff2: mdiff2 differences in Da applied to IFC chromatogram drawing " ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="myfile: name of the output file default halo_list.csv" ),columnspan=2, sticky="w")
tkgrid(tklabel(HELPFrame,text="myfile2: name of the output file default halo_list_short.csv is a resume from all individual myfile\n in the case off several files have been processed " ),columnspan=2, sticky="w")
tkgrid(HELPFrame, sticky="we")
#
# User closed the window
#
if(tclvalue(done)=="2") return()
}
}
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