R/report-utils-tex.R
In fbreitwieser/isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data
#################################################
## Helper Functions for LaTeX Report Generation
load.tex.properties <- function(env) {
get.property <- function(name) { get(name,env$properties.env,inherits=FALSE) }
if (!exists("properties.env",envir=env)) {
warning("No properties.env - loading properties")
assign("properties.env",load.properties(),envir=env)
}
needed.objects <- c('ibspectra','noise.model','quant.tbl','ratiodistr')
if (!all(needed.objects %in% objects(envir=env))) {
warning("Not all necessary objects present - calling initialize.env")
initialize.env(env,env$properties.env)
}
assign("get.property",get.property,envir=env)
}
write.tex.commands <- function() {
get.property <- get("get.property")
cat("\\newcommand{\\analysisname}{",sanitize(get.property('name'),dash=FALSE),"}\n")
cat("\\newcommand{\\analysisauthor}{",sanitize(get.property('author'),dash=FALSE),"}\n")
cat("\\newcommand{\\isobarthanks}{\\thanks{This report was
generated using the \\texttt{isobar} R package version ",
packageDescription("isobar")$Version,
" [built using ",packageDescription("isobar")$Built,"]",
". If you use it in published work, please cite ",
"'Breitwieser FP \\textit{et~al.}: General statistical ",
" modeling of data from protein relative expression isobaric tags, ",
" \\textit{Journal of Proteome Research} 2011' and ",
"'Breitwieser FP and Colinge J: isobarPTM: A software tool for the quantitative analysis of post-translationally modified proteins,",
"\\textit{Journal of Proteomics} 2013","'}}\n",sep="")
}
print_longtablehdr <- function(level,is.single.comparision,is.quant.tbl,file="") {
draw.channels <- !is.single.comparision
draw.signcol <- is.quant.tbl
if (is.single.comparision) {
coldef <- "@{}rXfrrrr@{}r@{}r@{}"
coldef.s <- "@{}rXfrrrr@{}r@{}"
ncol.p <- 9
} else {
coldef <- "@{}rXfrrrrrrr@{}r@{}"
coldef.s <- "@{}rXfrrrrrrr@{}"
ncol.p <- 11
}
if (!is.quant.tbl) {
coldef <- coldef.s
ncol.p <- ncol.p -1
}
mycat <- function(...,append=TRUE,sep="")
cat(...,file=file,append=append,sep=sep)
mycat("\\begin{longtable}{",coldef,"}\n",
" \\# ",paste(" & \\textbf{",level,"}")," & \\rh{group}",
" & \\rh{peptides}"," & \\rh{spectra}",append=FALSE)
# no ch1/ch2 columns when only one comparision available
if (draw.channels)
mycat("\n & \\rh{ch1} & \\rh{ch2}")
mycat("\n & \\rh{quant} & \\textbf{ratio}")
if (draw.signcol)
mycat(" & ")
mycat("\n & {\\hfill \\drawaxis{3pt}{south}}",
"\n\\endhead \n",rep(" &", ncol.p-1),
" {\\hfill \\drawaxis{-3pt}{north}}",
"\n \\endfoot \n")
}
print_longtablehdr_peptide <- function(coldef,draw.channels,ncol.p,draw.signcol) {
#cat("\n\n\\renewcommand{\\arraystretch}{0.75}\n")
cat("\\begin{longtable}{",coldef,"}",'\n',sep="")
cat("\t \\# ",paste(" & \\textbf{peptide}"))
# no ch1/ch2 columns when only one comparision available
if (draw.channels) {
cat('\n')
cat(" & \\rh{ch1}",
" & \\rh{ch2}",sep="\n\t")
}
cat("\n\t"," & \\rh{quant}")
cat("\n\t"," & \\textbf{ratio}")
if (draw.signcol) {
cat("\n\t"," & ")
#cat("\n\t"," & \\textbf{*}")
}
cat("\n\t"," & {\\hfill \\drawaxis{3pt}{south}}",
"\n \\endhead \n",rep(" &", ncol.p-1),
" {\\hfill \\drawaxis{-3pt}{north}}",
"\n \\endfoot \n")
}
draw.boxplot <- function(lratio,sd,bnd) {
if (is.na(lratio) || is.na(sd) || !is.finite(lratio) || !is.finite(sd)) {
return("")
}
ratio.smaller.bnd <- lratio - sd < -bnd
ratio.bigger.bnd <- lratio + sd > bnd
return(sprintf("\\boxplot{%.2f}{%.2f}{%s!%s}{%s}{%s}{%.0f}\n",
lratio,
sd,
ifelse(lratio > 0,"green","red"),
min(floor(abs(lratio)/bnd*100),100),
ifelse(ratio.smaller.bnd, "\\divcol", "black!1"),
ifelse(ratio.bigger.bnd, "\\divcol", "black!1"),
sd))
}
transform_pepmodif <- function(pep.n.modif) {
message(paste(pep.n.modif,collapse=" - "))
pep <- strsplit(pep.n.modif[1],"")[[1]]
modif <- strsplit(pep.n.modif[2],":")[[1]]
if (length(pep)+1 != length(modif))
stop("lengthwise i dont like them: ",pep.n.modif[1],
" and ",pep.n.modif[2])
# if (modif[length(modif)] != "")
# stop("modif contains something in the end:",
# pep.n.modif[2])
modif <- modif[seq(from=2,to=length(modif))]
pos <- as.numeric(sapply(modif,function(m) which(modifs[,1] == m)))
pep[!is.na(pos)] <- paste("\\pdftooltip{\\textcolor{",modifs[pos[!is.na(pos)],3],
"}{\\underline{",pep[!is.na(pos)],"}}}{",
modifs[pos[!is.na(pos)],1],"}",sep="")
return(paste(pep,collapse=""))
}
modifs <-
matrix(c(
"iTRAQ4plex_Nterm","i","black",
"iTRAQ4plex_K","i","black",
"Oxidation_M","o","black",
"Cys_CAM","c","black",
"PHOS","c","purple"),
byrow=TRUE,ncol=3)
.bnds <- function(x,bnd=NULL,min.x=-bnd,max.x=bnd) {
max(
min(x,max.x),
min.x)
}
# tex helper functions
draw.proteingroup.row <- function(name,protein.group,reporter.protein.g,file=file) {
mycat <- function(...,append=TRUE,sep="")
cat(...,file=file,append=append,sep=sep)
gmp <- groupMemberPeptides(protein.group,reporter.protein.g,TRUE)
pgt <- proteinGroupTable(protein.group)
n.multirow <- length(unique(protein.ac(protein.group,pgt[pgt$reporter.protein==reporter.protein.g,"protein.g"])))
mycat(name,"&",sep=" ")
n.row <- 1
show.pos <- TRUE
for (protein.i in seq_len(ncol(gmp$group.member.peptides))) {
x = colnames(gmp$group.member.peptides)[protein.i]
my.protein.info <- my.protein.info(protein.group,x)
my.acs <- unique(my.protein.info$accession)
for (ac.i in seq_along(my.acs)) {
if (n.row > 1) mycat(" & ")
sel <- my.protein.info$accession == my.acs[ac.i]
var.string <- number.ranges(my.protein.info$splicevariant[sel])
#cat(protein.i,"&")
if (show.pos && ncol(gmp$group.member.peptides)>1) {
if (ac.i == 1)
mycat("{\\small (",protein.i,")}",sep="")
else
mycat ("$\\mathord{\\cdot}$")
}
mycat(" & ")
mycat(sprintf("\\uniprotlink{%s}%s",sanitize(my.acs[ac.i],dash=FALSE),ifelse(is.na(var.string),"",paste0("-",var.string)[1])),
sanitize(unique(my.protein.info$gene_name[sel]))[1],
sanitize(unique(my.protein.info$protein_name[sel]))[1],
sep=", ")
if (n.row==1) {
# PEPTIDE GROUPING
mycat(" & ")
if (n.multirow > 1) mycat(" \\multirow{",n.multirow ,"}{*}{%\n",sep="")
mycat(tikz.proteingroup(protein.group,reporter.protein.g,show.pos,show.header=FALSE))
if (n.multirow > 1) mycat(" }")
mycat(" \\\\ \n")
} else {
mycat(" & \\\\ \n")
}
n.row <- n.row + 1
}
#human.protein.name <- human.protein.names(my.protein.info)
}
}
draw.protein.group <- function(protein.group,reporter.protein.g) {
gmp <- groupMemberPeptides(protein.group,reporter.protein.g,TRUE)
pgt <- proteinGroupTable(protein.group)
show.pos <- ncol(gmp$group.member.peptides) > 1
# cat("\\paragraph{Proteins}\n")
if (show.pos) {
cat("\\begin{tabular}{rl@{}llp{5cm}l}\n")
cat(paste("pos","accession","","gene name","protein name",sep=" & "))
} else {
cat("\\begin{tabular}{l@{}llp{5.5cm}l}\n")
cat(paste("accession","","gene name","protein name",sep=" & "))
}
cat(" & \\multirow{",length(unique(protein.ac(protein.group,
pgt[pgt$reporter.protein==reporter.protein.g,"protein.g"])))+1,
"}{*}{%\n",sep="")
tikz.proteingroup(protein.group,reporter.protein.g,show.pos)
cat("} \\\\ \n")
for (protein.i in seq_len(ncol(gmp$group.member.peptides))) {
x = colnames(gmp$group.member.peptides)[protein.i]
my.protein.info <- my.protein.info(protein.group,x)
for (ac in unique(my.protein.info$accession)) {
sel <- my.protein.info$accession == ac
var.string <- number.ranges(my.protein.info$splicevariant[sel])
if (show.pos) cat(protein.i,"&")
cat(paste(sprintf("\\uniprotlink{%s}",sanitize(ac,dash=FALSE)),
ifelse(is.na(var.string),"",var.string),
sanitize(unique(my.protein.info$gene_name[sel])),
sanitize(unique(my.protein.info$protein_name[sel])),"",
sep=" & "),"\\\\ \n")
}
#human.protein.name <- human.protein.names(my.protein.info)
}
cat("\\end{tabular}\n")
}
tikz.proteingroup <- function(protein.group,reporter.protein.g,show.pos,show.header=TRUE,
colors=c("blue","red","green","cyan","magenta","yellow")) {
gmp <- groupMemberPeptides(protein.group,reporter.protein.g,TRUE)
reporter.sp.sel <- gmp$peptide.info$specificity == "reporter-specific"
quant.sel <- gmp$peptide.info$n.shared.groups == 1 &
gmp$peptide.info$n.shared.proteins == 2
group.sp.sel <- gmp$peptide.info$specificity == "group-specific" & !quant.sel
unspecific.sel <- gmp$peptide.info$specificity == "unspecific"
peptide.styles <- rep("us",nrow(gmp$peptide.info))
peptide.styles[reporter.sp.sel] <- "rs"
peptide.styles[group.sp.sel] <- "gs"
res <- c()
gd.proteins <- apply(gmp$group.member.peptides[quant.sel,,drop=FALSE],2,any)
col.i <- 1
for (quant.prot.g in names(gd.proteins)[gd.proteins]) {
if (quant.prot.g != reporter.protein.g) {
quant.p.sel <- quant.sel & gmp$group.member.peptides[,quant.prot.g]
peptide.styles[quant.p.sel] <- sprintf("gs %s",colors[col.i])
if (col.i == length(colors)) {
col.i <- 1
} else {
col.i <- col.i + 1
}
}
}
n.peptides <- length(reporter.sp.sel)
max.n.peptides <- 10
tikz.y <- 0.5
tikz.x <- 0.4
tikz.minnodesize <- 0.2
if (n.peptides > max.n.peptides) {
tikz.x <- round(tikz.x*max.n.peptides/n.peptides,2)
tikz.minnodesize <- round(tikz.minnodesize*max.n.peptides/n.peptides,2)
}
res <- paste(res,sprintf("\\begin{tikzpicture}[x=%scm,y=%scm,every node/.style={minimum size=%scm}]\n",tikz.x,tikz.y,tikz.minnodesize))
if (show.header)
res <- paste(res," \\node at (1,0)[anchor=west] {peptides};\n")
n.groupmember <- ncol(gmp$group.member.peptides)
protein.peptides.df <- data.frame(
i=seq_len(n.groupmember),
rs=0,
gs=0,
us=0)
for (protein.i in seq_len(n.groupmember)) {
x = colnames(gmp$group.member.peptides)[protein.i]
my.protein.info <- my.protein.info(protein.group,x)
human.protein.name <- human.protein.names(my.protein.info)
name.i <- 1
table.name.nolink <- human.protein.name$ac_nolink[1]
nch.tablename <- nchar(table.name.nolink)
while (name.i < length(human.protein.name$ac_link)) {
nch.tablename <- nch.tablename + nchar(human.protein.name$ac_nolink[name.i])
if (nch.tablename < 20) {
table.name.nolink <- paste(table.name.nolink,
human.protein.name$ac_nolink[name.i],sep=",")
} else {
table.name.nolink <- paste(table.name.nolink,"\\dots",sep=",")
name.i <- Inf
}
name.i <- name.i + 1
}
peptide.idx.sel <- gmp$group.member.peptides[,protein.i]
protein.peptides.df[protein.i,] <- c(protein.i,
sum(peptide.idx.sel&reporter.sp.sel),
sum(peptide.idx.sel&(group.sp.sel|quant.sel)),
sum(peptide.idx.sel&unspecific.sel))
res<- paste(res,.print.proteinrow(
-protein.i,paste(which(peptide.idx.sel),peptide.styles[peptide.idx.sel],sep="/")
))
if (n.peptides < 15) {
res <- paste(res,connect.nodes(-protein.i,which((reporter.sp.sel | group.sp.sel | unspecific.sel | quant.sel)&gmp$group.member.peptides[,protein.i])))
}
}
res <- paste(res,sprintf(" \\node [left=.25cm of prot-1 pep1] {%s/%s/%s};\n",
sum(reporter.sp.sel),
sum(group.sp.sel),
sum(unspecific.sel)))
if (show.header) {
res <- paste(res,"\n"," \\matrix[ampersand replacement=\\&,matrix anchor=us node.east,anchor=base] at (0,0) {\n")
res <- paste(res,"\n"," \\node{}; \\& \\node {rs}; \\& \\node {gs}; \\& \\node (us node){us}; \\\\\n")
for (protein.i in seq_len(n.groupmember)) {
if (show.pos) res <- paste(res,"\n",sprintf(" \\node[draw,gray]{%s};",protein.i))
res <- paste(res,"\n",sprintf(" \\& \\node{%s};\\& \\node{%s};\\& \\node{%s}; \\\\\n",
protein.peptides.df[protein.i,"rs"],
protein.peptides.df[protein.i,"gs"],
protein.peptides.df[protein.i,"us"]))
}
res <- paste(res,"\n"," };\n")
}
res <- paste(res,"\\end{tikzpicture}\n")
return(res)
}
.tex.combinenames <- function(protein_name,is.single.comparision,cmbn) {
gene.names <- c()
for (prot.gene.name in protein_name) {
if (is.na(prot.gene.name)) next;
prot.gene.name <- ifelse(nchar(prot.gene.name)>80,
paste(sanitize(substr(prot.gene.name,0,76)),"\\dots"),
sanitize(prot.gene.name))
gene.names <- c(gene.names,prot.gene.name)
}
if (!is.single.comparision) {
if (length(gene.names) > ncol(cmbn) - 1) {
gene.names <- gene.names[seq_len(ncol(cmbn)-1)]
gene.names[length(gene.names)] <- paste(gene.names[length(gene.names)],", \\dots",sep="")
}
}
return(gene.names)
}
.print.proteinrow <- function(protein.idx,peptides.sel) {
if (length(peptides.sel)>0) {
sprintf(" \\proteinrow{%s}{%s}{}\n",
protein.idx,paste(peptides.sel,collapse=","))
}
}
connect.nodes <- function(protein.idx,pep.pos) {
if (length(pep.pos) == 1) return();
# message(protein.idx," (",length(pep.pos),"): ",paste(pep.pos,collapse=","),"\n")
last_pos = pep.pos[1];
res <- sprintf(" \\draw (prot%s pep%s)",protein.idx,last_pos)
for (i in 2:length(pep.pos)) {
if (pep.pos[i] == (last_pos+1)) {
res <- paste(res,"--")
}
last_pos <- pep.pos[i]
res <- paste(res,sprintf("(prot%s pep%s)",protein.idx,last_pos))
}
paste(res,";\n")
}
# function adapted from iquantitator
sanitize <- function(str,dash=TRUE) {
result <- str
result <- gsub("\\\\", "SANITIZE.BACKSLASH", result)
result <- gsub("$", "\\$", result, fixed = TRUE)
if (dash)
result <- gsub("-", "\\nobreakdash-", result, fixed = TRUE)
result <- gsub(">", "$>$", result, fixed = TRUE)
result <- gsub("<", "$<$", result, fixed = TRUE)
result <- gsub("|", "$|$", result, fixed = TRUE)
result <- gsub("{", "\\{", result, fixed = TRUE)
result <- gsub("}", "\\}", result, fixed = TRUE)
result <- gsub("%", "\\%", result, fixed = TRUE)
result <- gsub("&", "\\&", result, fixed = TRUE)
result <- gsub("_", "\\_", result, fixed = TRUE)
result <- gsub("#", "\\#", result, fixed = TRUE)
result <- gsub("^", "\\verb|^|", result, fixed = TRUE)
result <- gsub("~", "\\~{}", result, fixed = TRUE)
result <- gsub("SANITIZE.BACKSLASH", "$\\backslash$", result, fixed = TRUE)
return(result)
}
print_sign_proteins_tbl <- function(file,cmbn,protein.group,quant.tbl,my.protein.infos,bnd) {
is.single.comparision <- ncol(cmbn) ==1
mycat <- function(...,append=TRUE,sep="")
cat(...,file=file,append=append,sep=sep)
print_longtablehdr("protein",is.single.comparision,FALSE,file=file)
draw.hline <- FALSE
for (cmb_i in seq_len(ncol(cmbn))) {
sel <- quant.tbl[["r1"]]==cmbn[1,cmb_i] &
quant.tbl[["r2"]]==cmbn[2,cmb_i] &
quant.tbl[["is.significant"]] == 1
sel[is.na(sel)] <- FALSE
if (any(sel)) {
if (draw.hline) {
mycat (" \\hline\n")
} else {
draw.hline = TRUE
}
prot_i <- 1
proteins <- quant.tbl[sel,"ac"][order(quant.tbl[sel,"lratio"])]
for (protein in proteins) {
prot.info <- my.protein.infos[[protein]]
protein.row <- quant.tbl[quant.tbl[["ac"]]==protein & sel,,drop=FALSE]
reporter.peptides <- peptides(protein.group,protein=protein)
n.spectra <- length(names(spectrumToPeptide(protein.group))[spectrumToPeptide(protein.group)%in%reporter.peptides])
protein.names <- prot.info[["collapsed.gene_name"]][["protein_name"]]
gene.names <- .tex.combinenames(protein.names,is.single.comparision,cmbn)
mycat(" ",sprintf("\\hyperref[protein.%s]{%s}",
protein.row[,"group"],prot_i),
" & ",paste0(prot.info[["table.name"]],": ",
paste(gene.names,collapse=", ")),
" & ",print_groupsize(prot.info[["n.reporter"]],prot.info[["n.groupmember"]]),
" & ",length(reporter.peptides),
" & ",n.spectra)
if (!is.single.comparision) {
mycat(" & ",cmbn[1,cmb_i]," & ",cmbn[2,cmb_i])
}
mycat(" & ",protein.row[1,"n.spectra"])
mycat(" & ",sprintf("\\textbf{%.2f}",10^protein.row[1,"lratio"]),sep=" ")
mycat(" & ",draw.boxplot(protein.row[1,'lratio'],
protein.row[1,'sd'],bnd))
mycat(" \\\\ \n")
prot_i <- prot_i + 1
}
}
}
mycat("\\end{longtable}\n")
}
print_groupsize <- function (r,t) {
if (r>1 || t>1)
paste0(r,"/",t)
}
get_n_proteins <- function(quant.tbl,sign=FALSE,is.na=FALSE) {
n.quant <- ddply(quant.tbl,
c("class1","class2"),
function(x) {
sel <- !is.na(x[["lratio"]])
if (is.na) sel <- !sel
if (sign) sel <- sel & x[["is.significant"]]
sum(sel)
})
n.quant <- n.quant[n.quant[["V1"]]>0,]
paste(sprintf("%s/%s: %s",
sanitize(n.quant[["class2"]]),
sanitize(n.quant[["class1"]]),
n.quant[["V1"]]),collapse="; ")
}
print_protein_quant_tbl <- function(file="",
cmbn,protein.group,
quant.tbl,
my.protein.infos,
bnd) {
message("Writing protein quantifications table ... ",append.lf=FALSE)
is.single.comparision <- ncol(cmbn) ==1
mycat <- function(...,append=TRUE,sep="")
cat(...,file=file,append=append,sep=sep)
mr <- function(text,...) if (is.single.comparision) { text } else { sprintf("\\mr{%s}",text) }
mrp <- function(text,...) if (is.single.comparision) { text } else {sprintf("\\mrp{%s}",text)}
print_longtablehdr("protein",is.single.comparision,TRUE,file=file)
proteins.n.group <- unique(quant.tbl[,c('ac','group')])
proteins <- proteins.n.group[order(proteins.n.group[["group"]]),"ac"]
for (protein in proteins) {
protein.rows <- quant.tbl[quant.tbl[["ac"]]==protein,,drop=FALSE]
protein.rows <- protein.rows[order(protein.rows[["r1"]],protein.rows[["r2"]]),,drop=FALSE]
protein.groupnumber <- protein.rows[1,"group"]
prot.info <- my.protein.infos[[protein]]
reporter.peptides <- peptides(protein.group,protein=protein)
spectra <- names(spectrumToPeptide(protein.group))[spectrumToPeptide(protein.group)%in%reporter.peptides]
if (all(is.na(protein.rows[,'lratio']))) {
next
}
protein.names <- prot.info[["collapsed.gene_name"]][["protein_name"]]
gene.names <- .tex.combinenames(protein.names,is.single.comparision,cmbn)
mycat(mr(sprintf(" \\hyperref[protein.%s]{\\textbf{%s}}",
protein.groupnumber,protein.groupnumber)),
" & ",mrp(paste0(prot.info[["table.name"]],ifelse(length(gene.names)>0,": ",""),
paste(gene.names,collapse=", "))),
# " & ",mr(paste(prot.info[["n.reporter"]],prot.info[["n.groupmember"]],sep="/")),
" & ",mr(print_groupsize(prot.info[["n.reporter"]],prot.info[["n.groupmember"]])),
" & ",mr(length(reporter.peptides)),
" & ",mr(length(spectra)),sep=" ")
for (i in seq_len(ncol(cmbn))) {
if (i > 1) { mycat(paste(rep("&",4),collapse=" ")) }
if (!is.single.comparision) {
mycat(" & ",protein.rows[i,'r1'])
mycat(" & ",protein.rows[i,'r2'])
}
mycat(" & ",ifelse(is.na(protein.rows[i,'n.spectra']) |
protein.rows[i,'n.spectra']==0,"",protein.rows[i,'n.spectra']))
if (is.na(protein.rows[i,"lratio"])) {
mycat (" & & & ")
} else {
mycat(" & ",sprintf("\\textbf{%.2f}",10^protein.rows[i,"lratio"]))
mycat(" & ",ifelse(protein.rows[i,"is.significant"] == 1,"*",""))
mycat(" & ",draw.boxplot(protein.rows[i,'lratio'],
protein.rows[i,'sd'],bnd))
}
mycat(" \\\\")
if (i < ncol(cmbn)) mycat("*\n")
}
if (protein != proteins[length(proteins)] && ncol(cmbn) > 1) {
mycat(" \\midrule[0.02em] \n\n");
}
}
mycat("\\end{longtable}\n")
message("done")
}
print_classlabels_tbl <- function(cl,reporterTagNames) {
if (!is.null(cl)) {
cl[is.na(cl)] <- ""
if (!is.null(cl)) {
if (is.null(names(cl))) {
cat("\\begin{tabular}{rp{4cm}}\n")
cat("Channel & Class \\\\ \\hline \\bigstrut[t]\n")
cl <- paste("\\emph{",cl,"}",sep="")
} else {
cat("\\begin{tabular}{rrM}\n")
cat("\\multicolumn{3}{c}{Class Labels} \\bigstrut \\\\ \n")
cat("Channel & Class & Description \\\\ \\hline \\bigstrut[t]\n")
cl <- paste(paste("\\emph{",cl,"} & "),names(cl),sep="")
}
for (i in seq_along(reporterTagNames)) {
cat(reporterTagNames[i]," & ",
cl[i],
"\\\\ \n")
}
cat("\\end{tabular}\n")
}
}
}
print_protein_notquant_tbl <- function(file="",
cmbn,protein.group,
quant.tbl,
my.protein.infos) {
is.single.comparision <- ncol(cmbn) ==1
mycat <- function(...,append=TRUE,sep="")
cat(...,file=file,append=append,sep=sep)
tt <- table(quant.tbl[is.na(quant.tbl[["lratio"]]),"ac"])
proteins.notquantified <- names(tt)[tt==ncol(cmbn)]
mycat("\\begin{longtable}{rXrrr}",
" \\#",
" & \\textbf{protein}",
" & \\rh{group}",
" & \\rh{peptides}",
" & \\rh{spectra}",
"\\endhead",sep="\n",append=FALSE)
for (protein in proteins.notquantified) {
protein.rows <- quant.tbl[quant.tbl[["ac"]]==protein,,drop=FALSE]
protein.rows <- protein.rows[order(protein.rows[["r1"]],protein.rows[["r2"]]),,drop=FALSE]
protein.groupnumber <- protein.rows[1,"group"]
prot.info <- my.protein.infos[[protein]]
reporter.peptides <- peptides(protein.group,protein=protein)
spectra <- names(spectrumToPeptide(protein.group))[spectrumToPeptide(protein.group)%in%reporter.peptides]
protein.names <- prot.info[["collapsed.gene_name"]][["protein_name"]]
gene.names <- .tex.combinenames(protein.names,is.single.comparision,cmbn)
mycat(sprintf(" \\hyperref[protein.%s]{%s}",
protein.groupnumber,protein.groupnumber),
" & ",paste0(prot.info[["table.name"]],": ",
paste(gene.names,collapse=", ")),
" & ",print_groupsize(prot.info[["n.reporter"]],prot.info[["n.groupmember"]]),
" & ",length(reporter.peptides),
" & ",length(spectra),"\\\\ \n",sep=" ")
}
mycat("\\end{longtable}\n")
}
print_protein_grp_tbl <- function(file="",proteins, protein.group) {
mycat <- function(...,append=TRUE,sep="")
cat(...,file=file,append=append,sep=sep)
mycat("\\begin{longtable}{rcXp{6cm}}\n",append=FALSE)
prot_i <- 1
for (reporter.protein.g in proteins) {
draw.proteingroup.row(sprintf("\\label{protein.%s} %s",prot_i,prot_i),protein.group,reporter.protein.g,file=file)
mycat("\\bigstrut\n")
if (prot_i%%100 == 0) message(".",appendLF=FALSE);
prot_i <- prot_i + 1
}
mycat("\\end{longtable}\n")
}
print_protein_grp_info <- function() {
cat("
\\section{Protein Group Details} \\label{sec:proteingroups}
Protein groups are created by grouping according to mass spectrometry evidence:
\\begin{tabularx}{\\textwidth}{rX}
1. & Proteins which are detected with the exact same set of peptides are clustered - they are indistinguishable based on available MS data. Very often these are splice variants. In the following text, proteins are clustered proteins (cluster size one if they have specific peptides). \\\\
2. & Proteins, which have unique peptides (\\emph{i.\\,e.}~peptides not present in other detected proteins) are promoted to \\emph{reporters}. \\\\
3. & Remaining proteins are grouped to those reporters which have a superset of the peptides they have. These proteins are termed \\emph{group members} \\\\
\\end{tabularx}
Peptides are characterized based on their specificity to one or more proteins, and one or more protein groups:
\\begin{center}
\\begin{tabular}{rll}
\\emph{reporter specific} rs & \\tikz \\node[rs,minimum size=0.2cm] {}; & Number of peptides specific to reporter. \\\\
\\emph{group specific} gs & \\tikz \\node[gs,minimum size=0.2cm] {}; & Number of peptides specific to the group (including rs). \\\\
\\emph{unspecific} us & \\tikz \\node[us,minimum size=0.2cm] {}; & Number of peptides shared with any protein. \\\\
\\end{tabular}
\\end{center}
")
}
fbreitwieser/isobar documentation built on May 16, 2019, 12:01 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#################################################
## Helper Functions for LaTeX Report Generation
load.tex.properties <- function(env) {
get.property <- function(name) { get(name,env$properties.env,inherits=FALSE) }
if (!exists("properties.env",envir=env)) {
warning("No properties.env - loading properties")
assign("properties.env",load.properties(),envir=env)
}
needed.objects <- c('ibspectra','noise.model','quant.tbl','ratiodistr')
if (!all(needed.objects %in% objects(envir=env))) {
warning("Not all necessary objects present - calling initialize.env")
initialize.env(env,env$properties.env)
}
assign("get.property",get.property,envir=env)
}
write.tex.commands <- function() {
get.property <- get("get.property")
cat("\\newcommand{\\analysisname}{",sanitize(get.property('name'),dash=FALSE),"}\n")
cat("\\newcommand{\\analysisauthor}{",sanitize(get.property('author'),dash=FALSE),"}\n")
cat("\\newcommand{\\isobarthanks}{\\thanks{This report was
generated using the \\texttt{isobar} R package version ",
packageDescription("isobar")$Version,
" [built using ",packageDescription("isobar")$Built,"]",
". If you use it in published work, please cite ",
"'Breitwieser FP \\textit{et~al.}: General statistical ",
" modeling of data from protein relative expression isobaric tags, ",
" \\textit{Journal of Proteome Research} 2011' and ",
"'Breitwieser FP and Colinge J: isobarPTM: A software tool for the quantitative analysis of post-translationally modified proteins,",
"\\textit{Journal of Proteomics} 2013","'}}\n",sep="")
}
print_longtablehdr <- function(level,is.single.comparision,is.quant.tbl,file="") {
draw.channels <- !is.single.comparision
draw.signcol <- is.quant.tbl
if (is.single.comparision) {
coldef <- "@{}rXfrrrr@{}r@{}r@{}"
coldef.s <- "@{}rXfrrrr@{}r@{}"
ncol.p <- 9
} else {
coldef <- "@{}rXfrrrrrrr@{}r@{}"
coldef.s <- "@{}rXfrrrrrrr@{}"
ncol.p <- 11
}
if (!is.quant.tbl) {
coldef <- coldef.s
ncol.p <- ncol.p -1
}
mycat <- function(...,append=TRUE,sep="")
cat(...,file=file,append=append,sep=sep)
mycat("\\begin{longtable}{",coldef,"}\n",
" \\# ",paste(" & \\textbf{",level,"}")," & \\rh{group}",
" & \\rh{peptides}"," & \\rh{spectra}",append=FALSE)
# no ch1/ch2 columns when only one comparision available
if (draw.channels)
mycat("\n & \\rh{ch1} & \\rh{ch2}")
mycat("\n & \\rh{quant} & \\textbf{ratio}")
if (draw.signcol)
mycat(" & ")
mycat("\n & {\\hfill \\drawaxis{3pt}{south}}",
"\n\\endhead \n",rep(" &", ncol.p-1),
" {\\hfill \\drawaxis{-3pt}{north}}",
"\n \\endfoot \n")
}
print_longtablehdr_peptide <- function(coldef,draw.channels,ncol.p,draw.signcol) {
#cat("\n\n\\renewcommand{\\arraystretch}{0.75}\n")
cat("\\begin{longtable}{",coldef,"}",'\n',sep="")
cat("\t \\# ",paste(" & \\textbf{peptide}"))
# no ch1/ch2 columns when only one comparision available
if (draw.channels) {
cat('\n')
cat(" & \\rh{ch1}",
" & \\rh{ch2}",sep="\n\t")
}
cat("\n\t"," & \\rh{quant}")
cat("\n\t"," & \\textbf{ratio}")
if (draw.signcol) {
cat("\n\t"," & ")
#cat("\n\t"," & \\textbf{*}")
}
cat("\n\t"," & {\\hfill \\drawaxis{3pt}{south}}",
"\n \\endhead \n",rep(" &", ncol.p-1),
" {\\hfill \\drawaxis{-3pt}{north}}",
"\n \\endfoot \n")
}
draw.boxplot <- function(lratio,sd,bnd) {
if (is.na(lratio) || is.na(sd) || !is.finite(lratio) || !is.finite(sd)) {
return("")
}
ratio.smaller.bnd <- lratio - sd < -bnd
ratio.bigger.bnd <- lratio + sd > bnd
return(sprintf("\\boxplot{%.2f}{%.2f}{%s!%s}{%s}{%s}{%.0f}\n",
lratio,
sd,
ifelse(lratio > 0,"green","red"),
min(floor(abs(lratio)/bnd*100),100),
ifelse(ratio.smaller.bnd, "\\divcol", "black!1"),
ifelse(ratio.bigger.bnd, "\\divcol", "black!1"),
sd))
}
transform_pepmodif <- function(pep.n.modif) {
message(paste(pep.n.modif,collapse=" - "))
pep <- strsplit(pep.n.modif[1],"")[[1]]
modif <- strsplit(pep.n.modif[2],":")[[1]]
if (length(pep)+1 != length(modif))
stop("lengthwise i dont like them: ",pep.n.modif[1],
" and ",pep.n.modif[2])
# if (modif[length(modif)] != "")
# stop("modif contains something in the end:",
# pep.n.modif[2])
modif <- modif[seq(from=2,to=length(modif))]
pos <- as.numeric(sapply(modif,function(m) which(modifs[,1] == m)))
pep[!is.na(pos)] <- paste("\\pdftooltip{\\textcolor{",modifs[pos[!is.na(pos)],3],
"}{\\underline{",pep[!is.na(pos)],"}}}{",
modifs[pos[!is.na(pos)],1],"}",sep="")
return(paste(pep,collapse=""))
}
modifs <-
matrix(c(
"iTRAQ4plex_Nterm","i","black",
"iTRAQ4plex_K","i","black",
"Oxidation_M","o","black",
"Cys_CAM","c","black",
"PHOS","c","purple"),
byrow=TRUE,ncol=3)
.bnds <- function(x,bnd=NULL,min.x=-bnd,max.x=bnd) {
max(
min(x,max.x),
min.x)
}
# tex helper functions
draw.proteingroup.row <- function(name,protein.group,reporter.protein.g,file=file) {
mycat <- function(...,append=TRUE,sep="")
cat(...,file=file,append=append,sep=sep)
gmp <- groupMemberPeptides(protein.group,reporter.protein.g,TRUE)
pgt <- proteinGroupTable(protein.group)
n.multirow <- length(unique(protein.ac(protein.group,pgt[pgt$reporter.protein==reporter.protein.g,"protein.g"])))
mycat(name,"&",sep=" ")
n.row <- 1
show.pos <- TRUE
for (protein.i in seq_len(ncol(gmp$group.member.peptides))) {
x = colnames(gmp$group.member.peptides)[protein.i]
my.protein.info <- my.protein.info(protein.group,x)
my.acs <- unique(my.protein.info$accession)
for (ac.i in seq_along(my.acs)) {
if (n.row > 1) mycat(" & ")
sel <- my.protein.info$accession == my.acs[ac.i]
var.string <- number.ranges(my.protein.info$splicevariant[sel])
#cat(protein.i,"&")
if (show.pos && ncol(gmp$group.member.peptides)>1) {
if (ac.i == 1)
mycat("{\\small (",protein.i,")}",sep="")
else
mycat ("$\\mathord{\\cdot}$")
}
mycat(" & ")
mycat(sprintf("\\uniprotlink{%s}%s",sanitize(my.acs[ac.i],dash=FALSE),ifelse(is.na(var.string),"",paste0("-",var.string)[1])),
sanitize(unique(my.protein.info$gene_name[sel]))[1],
sanitize(unique(my.protein.info$protein_name[sel]))[1],
sep=", ")
if (n.row==1) {
# PEPTIDE GROUPING
mycat(" & ")
if (n.multirow > 1) mycat(" \\multirow{",n.multirow ,"}{*}{%\n",sep="")
mycat(tikz.proteingroup(protein.group,reporter.protein.g,show.pos,show.header=FALSE))
if (n.multirow > 1) mycat(" }")
mycat(" \\\\ \n")
} else {
mycat(" & \\\\ \n")
}
n.row <- n.row + 1
}
#human.protein.name <- human.protein.names(my.protein.info)
}
}
draw.protein.group <- function(protein.group,reporter.protein.g) {
gmp <- groupMemberPeptides(protein.group,reporter.protein.g,TRUE)
pgt <- proteinGroupTable(protein.group)
show.pos <- ncol(gmp$group.member.peptides) > 1
# cat("\\paragraph{Proteins}\n")
if (show.pos) {
cat("\\begin{tabular}{rl@{}llp{5cm}l}\n")
cat(paste("pos","accession","","gene name","protein name",sep=" & "))
} else {
cat("\\begin{tabular}{l@{}llp{5.5cm}l}\n")
cat(paste("accession","","gene name","protein name",sep=" & "))
}
cat(" & \\multirow{",length(unique(protein.ac(protein.group,
pgt[pgt$reporter.protein==reporter.protein.g,"protein.g"])))+1,
"}{*}{%\n",sep="")
tikz.proteingroup(protein.group,reporter.protein.g,show.pos)
cat("} \\\\ \n")
for (protein.i in seq_len(ncol(gmp$group.member.peptides))) {
x = colnames(gmp$group.member.peptides)[protein.i]
my.protein.info <- my.protein.info(protein.group,x)
for (ac in unique(my.protein.info$accession)) {
sel <- my.protein.info$accession == ac
var.string <- number.ranges(my.protein.info$splicevariant[sel])
if (show.pos) cat(protein.i,"&")
cat(paste(sprintf("\\uniprotlink{%s}",sanitize(ac,dash=FALSE)),
ifelse(is.na(var.string),"",var.string),
sanitize(unique(my.protein.info$gene_name[sel])),
sanitize(unique(my.protein.info$protein_name[sel])),"",
sep=" & "),"\\\\ \n")
}
#human.protein.name <- human.protein.names(my.protein.info)
}
cat("\\end{tabular}\n")
}
tikz.proteingroup <- function(protein.group,reporter.protein.g,show.pos,show.header=TRUE,
colors=c("blue","red","green","cyan","magenta","yellow")) {
gmp <- groupMemberPeptides(protein.group,reporter.protein.g,TRUE)
reporter.sp.sel <- gmp$peptide.info$specificity == "reporter-specific"
quant.sel <- gmp$peptide.info$n.shared.groups == 1 &
gmp$peptide.info$n.shared.proteins == 2
group.sp.sel <- gmp$peptide.info$specificity == "group-specific" & !quant.sel
unspecific.sel <- gmp$peptide.info$specificity == "unspecific"
peptide.styles <- rep("us",nrow(gmp$peptide.info))
peptide.styles[reporter.sp.sel] <- "rs"
peptide.styles[group.sp.sel] <- "gs"
res <- c()
gd.proteins <- apply(gmp$group.member.peptides[quant.sel,,drop=FALSE],2,any)
col.i <- 1
for (quant.prot.g in names(gd.proteins)[gd.proteins]) {
if (quant.prot.g != reporter.protein.g) {
quant.p.sel <- quant.sel & gmp$group.member.peptides[,quant.prot.g]
peptide.styles[quant.p.sel] <- sprintf("gs %s",colors[col.i])
if (col.i == length(colors)) {
col.i <- 1
} else {
col.i <- col.i + 1
}
}
}
n.peptides <- length(reporter.sp.sel)
max.n.peptides <- 10
tikz.y <- 0.5
tikz.x <- 0.4
tikz.minnodesize <- 0.2
if (n.peptides > max.n.peptides) {
tikz.x <- round(tikz.x*max.n.peptides/n.peptides,2)
tikz.minnodesize <- round(tikz.minnodesize*max.n.peptides/n.peptides,2)
}
res <- paste(res,sprintf("\\begin{tikzpicture}[x=%scm,y=%scm,every node/.style={minimum size=%scm}]\n",tikz.x,tikz.y,tikz.minnodesize))
if (show.header)
res <- paste(res," \\node at (1,0)[anchor=west] {peptides};\n")
n.groupmember <- ncol(gmp$group.member.peptides)
protein.peptides.df <- data.frame(
i=seq_len(n.groupmember),
rs=0,
gs=0,
us=0)
for (protein.i in seq_len(n.groupmember)) {
x = colnames(gmp$group.member.peptides)[protein.i]
my.protein.info <- my.protein.info(protein.group,x)
human.protein.name <- human.protein.names(my.protein.info)
name.i <- 1
table.name.nolink <- human.protein.name$ac_nolink[1]
nch.tablename <- nchar(table.name.nolink)
while (name.i < length(human.protein.name$ac_link)) {
nch.tablename <- nch.tablename + nchar(human.protein.name$ac_nolink[name.i])
if (nch.tablename < 20) {
table.name.nolink <- paste(table.name.nolink,
human.protein.name$ac_nolink[name.i],sep=",")
} else {
table.name.nolink <- paste(table.name.nolink,"\\dots",sep=",")
name.i <- Inf
}
name.i <- name.i + 1
}
peptide.idx.sel <- gmp$group.member.peptides[,protein.i]
protein.peptides.df[protein.i,] <- c(protein.i,
sum(peptide.idx.sel&reporter.sp.sel),
sum(peptide.idx.sel&(group.sp.sel|quant.sel)),
sum(peptide.idx.sel&unspecific.sel))
res<- paste(res,.print.proteinrow(
-protein.i,paste(which(peptide.idx.sel),peptide.styles[peptide.idx.sel],sep="/")
))
if (n.peptides < 15) {
res <- paste(res,connect.nodes(-protein.i,which((reporter.sp.sel | group.sp.sel | unspecific.sel | quant.sel)&gmp$group.member.peptides[,protein.i])))
}
}
res <- paste(res,sprintf(" \\node [left=.25cm of prot-1 pep1] {%s/%s/%s};\n",
sum(reporter.sp.sel),
sum(group.sp.sel),
sum(unspecific.sel)))
if (show.header) {
res <- paste(res,"\n"," \\matrix[ampersand replacement=\\&,matrix anchor=us node.east,anchor=base] at (0,0) {\n")
res <- paste(res,"\n"," \\node{}; \\& \\node {rs}; \\& \\node {gs}; \\& \\node (us node){us}; \\\\\n")
for (protein.i in seq_len(n.groupmember)) {
if (show.pos) res <- paste(res,"\n",sprintf(" \\node[draw,gray]{%s};",protein.i))
res <- paste(res,"\n",sprintf(" \\& \\node{%s};\\& \\node{%s};\\& \\node{%s}; \\\\\n",
protein.peptides.df[protein.i,"rs"],
protein.peptides.df[protein.i,"gs"],
protein.peptides.df[protein.i,"us"]))
}
res <- paste(res,"\n"," };\n")
}
res <- paste(res,"\\end{tikzpicture}\n")
return(res)
}
.tex.combinenames <- function(protein_name,is.single.comparision,cmbn) {
gene.names <- c()
for (prot.gene.name in protein_name) {
if (is.na(prot.gene.name)) next;
prot.gene.name <- ifelse(nchar(prot.gene.name)>80,
paste(sanitize(substr(prot.gene.name,0,76)),"\\dots"),
sanitize(prot.gene.name))
gene.names <- c(gene.names,prot.gene.name)
}
if (!is.single.comparision) {
if (length(gene.names) > ncol(cmbn) - 1) {
gene.names <- gene.names[seq_len(ncol(cmbn)-1)]
gene.names[length(gene.names)] <- paste(gene.names[length(gene.names)],", \\dots",sep="")
}
}
return(gene.names)
}
.print.proteinrow <- function(protein.idx,peptides.sel) {
if (length(peptides.sel)>0) {
sprintf(" \\proteinrow{%s}{%s}{}\n",
protein.idx,paste(peptides.sel,collapse=","))
}
}
connect.nodes <- function(protein.idx,pep.pos) {
if (length(pep.pos) == 1) return();
# message(protein.idx," (",length(pep.pos),"): ",paste(pep.pos,collapse=","),"\n")
last_pos = pep.pos[1];
res <- sprintf(" \\draw (prot%s pep%s)",protein.idx,last_pos)
for (i in 2:length(pep.pos)) {
if (pep.pos[i] == (last_pos+1)) {
res <- paste(res,"--")
}
last_pos <- pep.pos[i]
res <- paste(res,sprintf("(prot%s pep%s)",protein.idx,last_pos))
}
paste(res,";\n")
}
# function adapted from iquantitator
sanitize <- function(str,dash=TRUE) {
result <- str
result <- gsub("\\\\", "SANITIZE.BACKSLASH", result)
result <- gsub("$", "\\$", result, fixed = TRUE)
if (dash)
result <- gsub("-", "\\nobreakdash-", result, fixed = TRUE)
result <- gsub(">", "$>$", result, fixed = TRUE)
result <- gsub("<", "$<$", result, fixed = TRUE)
result <- gsub("|", "$|$", result, fixed = TRUE)
result <- gsub("{", "\\{", result, fixed = TRUE)
result <- gsub("}", "\\}", result, fixed = TRUE)
result <- gsub("%", "\\%", result, fixed = TRUE)
result <- gsub("&", "\\&", result, fixed = TRUE)
result <- gsub("_", "\\_", result, fixed = TRUE)
result <- gsub("#", "\\#", result, fixed = TRUE)
result <- gsub("^", "\\verb|^|", result, fixed = TRUE)
result <- gsub("~", "\\~{}", result, fixed = TRUE)
result <- gsub("SANITIZE.BACKSLASH", "$\\backslash$", result, fixed = TRUE)
return(result)
}
print_sign_proteins_tbl <- function(file,cmbn,protein.group,quant.tbl,my.protein.infos,bnd) {
is.single.comparision <- ncol(cmbn) ==1
mycat <- function(...,append=TRUE,sep="")
cat(...,file=file,append=append,sep=sep)
print_longtablehdr("protein",is.single.comparision,FALSE,file=file)
draw.hline <- FALSE
for (cmb_i in seq_len(ncol(cmbn))) {
sel <- quant.tbl[["r1"]]==cmbn[1,cmb_i] &
quant.tbl[["r2"]]==cmbn[2,cmb_i] &
quant.tbl[["is.significant"]] == 1
sel[is.na(sel)] <- FALSE
if (any(sel)) {
if (draw.hline) {
mycat (" \\hline\n")
} else {
draw.hline = TRUE
}
prot_i <- 1
proteins <- quant.tbl[sel,"ac"][order(quant.tbl[sel,"lratio"])]
for (protein in proteins) {
prot.info <- my.protein.infos[[protein]]
protein.row <- quant.tbl[quant.tbl[["ac"]]==protein & sel,,drop=FALSE]
reporter.peptides <- peptides(protein.group,protein=protein)
n.spectra <- length(names(spectrumToPeptide(protein.group))[spectrumToPeptide(protein.group)%in%reporter.peptides])
protein.names <- prot.info[["collapsed.gene_name"]][["protein_name"]]
gene.names <- .tex.combinenames(protein.names,is.single.comparision,cmbn)
mycat(" ",sprintf("\\hyperref[protein.%s]{%s}",
protein.row[,"group"],prot_i),
" & ",paste0(prot.info[["table.name"]],": ",
paste(gene.names,collapse=", ")),
" & ",print_groupsize(prot.info[["n.reporter"]],prot.info[["n.groupmember"]]),
" & ",length(reporter.peptides),
" & ",n.spectra)
if (!is.single.comparision) {
mycat(" & ",cmbn[1,cmb_i]," & ",cmbn[2,cmb_i])
}
mycat(" & ",protein.row[1,"n.spectra"])
mycat(" & ",sprintf("\\textbf{%.2f}",10^protein.row[1,"lratio"]),sep=" ")
mycat(" & ",draw.boxplot(protein.row[1,'lratio'],
protein.row[1,'sd'],bnd))
mycat(" \\\\ \n")
prot_i <- prot_i + 1
}
}
}
mycat("\\end{longtable}\n")
}
print_groupsize <- function (r,t) {
if (r>1 || t>1)
paste0(r,"/",t)
}
get_n_proteins <- function(quant.tbl,sign=FALSE,is.na=FALSE) {
n.quant <- ddply(quant.tbl,
c("class1","class2"),
function(x) {
sel <- !is.na(x[["lratio"]])
if (is.na) sel <- !sel
if (sign) sel <- sel & x[["is.significant"]]
sum(sel)
})
n.quant <- n.quant[n.quant[["V1"]]>0,]
paste(sprintf("%s/%s: %s",
sanitize(n.quant[["class2"]]),
sanitize(n.quant[["class1"]]),
n.quant[["V1"]]),collapse="; ")
}
print_protein_quant_tbl <- function(file="",
cmbn,protein.group,
quant.tbl,
my.protein.infos,
bnd) {
message("Writing protein quantifications table ... ",append.lf=FALSE)
is.single.comparision <- ncol(cmbn) ==1
mycat <- function(...,append=TRUE,sep="")
cat(...,file=file,append=append,sep=sep)
mr <- function(text,...) if (is.single.comparision) { text } else { sprintf("\\mr{%s}",text) }
mrp <- function(text,...) if (is.single.comparision) { text } else {sprintf("\\mrp{%s}",text)}
print_longtablehdr("protein",is.single.comparision,TRUE,file=file)
proteins.n.group <- unique(quant.tbl[,c('ac','group')])
proteins <- proteins.n.group[order(proteins.n.group[["group"]]),"ac"]
for (protein in proteins) {
protein.rows <- quant.tbl[quant.tbl[["ac"]]==protein,,drop=FALSE]
protein.rows <- protein.rows[order(protein.rows[["r1"]],protein.rows[["r2"]]),,drop=FALSE]
protein.groupnumber <- protein.rows[1,"group"]
prot.info <- my.protein.infos[[protein]]
reporter.peptides <- peptides(protein.group,protein=protein)
spectra <- names(spectrumToPeptide(protein.group))[spectrumToPeptide(protein.group)%in%reporter.peptides]
if (all(is.na(protein.rows[,'lratio']))) {
next
}
protein.names <- prot.info[["collapsed.gene_name"]][["protein_name"]]
gene.names <- .tex.combinenames(protein.names,is.single.comparision,cmbn)
mycat(mr(sprintf(" \\hyperref[protein.%s]{\\textbf{%s}}",
protein.groupnumber,protein.groupnumber)),
" & ",mrp(paste0(prot.info[["table.name"]],ifelse(length(gene.names)>0,": ",""),
paste(gene.names,collapse=", "))),
# " & ",mr(paste(prot.info[["n.reporter"]],prot.info[["n.groupmember"]],sep="/")),
" & ",mr(print_groupsize(prot.info[["n.reporter"]],prot.info[["n.groupmember"]])),
" & ",mr(length(reporter.peptides)),
" & ",mr(length(spectra)),sep=" ")
for (i in seq_len(ncol(cmbn))) {
if (i > 1) { mycat(paste(rep("&",4),collapse=" ")) }
if (!is.single.comparision) {
mycat(" & ",protein.rows[i,'r1'])
mycat(" & ",protein.rows[i,'r2'])
}
mycat(" & ",ifelse(is.na(protein.rows[i,'n.spectra']) |
protein.rows[i,'n.spectra']==0,"",protein.rows[i,'n.spectra']))
if (is.na(protein.rows[i,"lratio"])) {
mycat (" & & & ")
} else {
mycat(" & ",sprintf("\\textbf{%.2f}",10^protein.rows[i,"lratio"]))
mycat(" & ",ifelse(protein.rows[i,"is.significant"] == 1,"*",""))
mycat(" & ",draw.boxplot(protein.rows[i,'lratio'],
protein.rows[i,'sd'],bnd))
}
mycat(" \\\\")
if (i < ncol(cmbn)) mycat("*\n")
}
if (protein != proteins[length(proteins)] && ncol(cmbn) > 1) {
mycat(" \\midrule[0.02em] \n\n");
}
}
mycat("\\end{longtable}\n")
message("done")
}
print_classlabels_tbl <- function(cl,reporterTagNames) {
if (!is.null(cl)) {
cl[is.na(cl)] <- ""
if (!is.null(cl)) {
if (is.null(names(cl))) {
cat("\\begin{tabular}{rp{4cm}}\n")
cat("Channel & Class \\\\ \\hline \\bigstrut[t]\n")
cl <- paste("\\emph{",cl,"}",sep="")
} else {
cat("\\begin{tabular}{rrM}\n")
cat("\\multicolumn{3}{c}{Class Labels} \\bigstrut \\\\ \n")
cat("Channel & Class & Description \\\\ \\hline \\bigstrut[t]\n")
cl <- paste(paste("\\emph{",cl,"} & "),names(cl),sep="")
}
for (i in seq_along(reporterTagNames)) {
cat(reporterTagNames[i]," & ",
cl[i],
"\\\\ \n")
}
cat("\\end{tabular}\n")
}
}
}
print_protein_notquant_tbl <- function(file="",
cmbn,protein.group,
quant.tbl,
my.protein.infos) {
is.single.comparision <- ncol(cmbn) ==1
mycat <- function(...,append=TRUE,sep="")
cat(...,file=file,append=append,sep=sep)
tt <- table(quant.tbl[is.na(quant.tbl[["lratio"]]),"ac"])
proteins.notquantified <- names(tt)[tt==ncol(cmbn)]
mycat("\\begin{longtable}{rXrrr}",
" \\#",
" & \\textbf{protein}",
" & \\rh{group}",
" & \\rh{peptides}",
" & \\rh{spectra}",
"\\endhead",sep="\n",append=FALSE)
for (protein in proteins.notquantified) {
protein.rows <- quant.tbl[quant.tbl[["ac"]]==protein,,drop=FALSE]
protein.rows <- protein.rows[order(protein.rows[["r1"]],protein.rows[["r2"]]),,drop=FALSE]
protein.groupnumber <- protein.rows[1,"group"]
prot.info <- my.protein.infos[[protein]]
reporter.peptides <- peptides(protein.group,protein=protein)
spectra <- names(spectrumToPeptide(protein.group))[spectrumToPeptide(protein.group)%in%reporter.peptides]
protein.names <- prot.info[["collapsed.gene_name"]][["protein_name"]]
gene.names <- .tex.combinenames(protein.names,is.single.comparision,cmbn)
mycat(sprintf(" \\hyperref[protein.%s]{%s}",
protein.groupnumber,protein.groupnumber),
" & ",paste0(prot.info[["table.name"]],": ",
paste(gene.names,collapse=", ")),
" & ",print_groupsize(prot.info[["n.reporter"]],prot.info[["n.groupmember"]]),
" & ",length(reporter.peptides),
" & ",length(spectra),"\\\\ \n",sep=" ")
}
mycat("\\end{longtable}\n")
}
print_protein_grp_tbl <- function(file="",proteins, protein.group) {
mycat <- function(...,append=TRUE,sep="")
cat(...,file=file,append=append,sep=sep)
mycat("\\begin{longtable}{rcXp{6cm}}\n",append=FALSE)
prot_i <- 1
for (reporter.protein.g in proteins) {
draw.proteingroup.row(sprintf("\\label{protein.%s} %s",prot_i,prot_i),protein.group,reporter.protein.g,file=file)
mycat("\\bigstrut\n")
if (prot_i%%100 == 0) message(".",appendLF=FALSE);
prot_i <- prot_i + 1
}
mycat("\\end{longtable}\n")
}
print_protein_grp_info <- function() {
cat("
\\section{Protein Group Details} \\label{sec:proteingroups}
Protein groups are created by grouping according to mass spectrometry evidence:
\\begin{tabularx}{\\textwidth}{rX}
1. & Proteins which are detected with the exact same set of peptides are clustered - they are indistinguishable based on available MS data. Very often these are splice variants. In the following text, proteins are clustered proteins (cluster size one if they have specific peptides). \\\\
2. & Proteins, which have unique peptides (\\emph{i.\\,e.}~peptides not present in other detected proteins) are promoted to \\emph{reporters}. \\\\
3. & Remaining proteins are grouped to those reporters which have a superset of the peptides they have. These proteins are termed \\emph{group members} \\\\
\\end{tabularx}
Peptides are characterized based on their specificity to one or more proteins, and one or more protein groups:
\\begin{center}
\\begin{tabular}{rll}
\\emph{reporter specific} rs & \\tikz \\node[rs,minimum size=0.2cm] {}; & Number of peptides specific to reporter. \\\\
\\emph{group specific} gs & \\tikz \\node[gs,minimum size=0.2cm] {}; & Number of peptides specific to the group (including rs). \\\\
\\emph{unspecific} us & \\tikz \\node[us,minimum size=0.2cm] {}; & Number of peptides shared with any protein. \\\\
\\end{tabular}
\\end{center}
")
}
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