Nothing
R/rshtml.r
In sapFinder: A package for variant peptides detection and visualization in shotgun proteomics.
Defines functions
.rshtml
.pepsummary
.writeBody_s
.writeHead_s
.writeHtml_s
# .writeHtml_s
#
# write the html;
#
# @author xsh
.writeHtml_s<-function(data,stat_list,pep.summary.path,
pro.summary.path,filename="myTest",wmlist,outdir)
{
page_dir=paste(outdir,.PAGE.DIR,sep="/");
filename=.concat(page_dir,"/", filename, ".html" );
file=file(filename,"w");
cat('<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"',
' "http://www.w3.org/TR/html4/loose.dtd">\n', file=file, sep="");
.write(.tag("html"),file);
.writeHead_s(file);
.writeBody_s(data,stat_list,pep.summary.path,pro.summary.path,
file,wmlist=wmlist);
.write(.tag("/html"),file);
close(file);
}
# .writeHead_i
#
# write the header partion;
#
# @author xsh
.writeHead_s<-function(file)
{
.write(.tag("head"),file);
meta<-'http-equiv="Content-Type" content="text/html; charset=utf-8"';
.write(.ctag("meta",other=meta),file);
.write(.tag("title"),"stat",.tag("/title"),file);
.write(.tag("script",
other=paste('type=\"text/javascript\" src=','"',
.JAVASCRIPT.DIR,"/",.JQUERY.MIN.JS,'"',sep="")),nobreak=TRUE, file);
.write( .tag("/script"), file );
.write(.tag("script",
other=paste('type=\"text/javascript\" src=','"',.JAVASCRIPT.DIR,
"/",.INDEX.JS,'"',sep="")),nobreak=TRUE, file);
.write( .tag("/script"), file );
.write(.tag("link",other=paste('rel="stylesheet" type="text/css" href=',
'"',.CSS.DIR,"/",.INDEX.CSS,'"',sep="")),nobreak=TRUE, file);
.write( .tag("/link"), file );
.write(.tag("style",other='type="text/css"'),
"html{overflow:auto;};body{position:relative;}",.tag("/style"),file);
.write(.tag("/head"),file);
}
# .writeBody_g
#
# write the body partion;
#
# @author xsh
.writeBody_s<-function(data,stat_list,
pep.summary.path,
pro.summary.path,
file,wmlist)
{
.write(.tag("body"),file);
.write(.tag("div",class="seq_cn1"),file);
.write(.tag("a",class="button contenttoggle",
other=.concat('title="Click to download" href="../',.DATA.DIR,'/',
basename(pep.summary.path),'"')),"Download peptide summary",
.tag("/a"),file);
.write(.tag("a",class="button contenttoggle",
other=.concat('title="Click to download" href="../',.DATA.DIR,'/',
basename(pro.summary.path),'"')),"Download protide summary",
.tag("/a"),file);
.write(.ctag("br"),.ctag("hr",class="clear-contentunit"),.ctag("br"),file);
.write(.tag("h1"),"Summary List",.tag("/h1"),.ctag("br"),file);
.write(.tag("div"),.tag("table",class="stat"),file);
.write(.tag("tbody"),file);
.write(.tag("tr"),file);
.write(.tag("th"),"Number of identified spectra :",.tag("/th"),file);
.write(.tag("td"),stat_list[["all_sp_num"]],.tag("/td"),file);
.write(.tag("/tr"),file);
.write(.tag("tr"),file);
.write(.tag("th"),"Number of identified peptide :",.tag("/th"),file);
.write(.tag("td"),stat_list[["all_pep_num"]],.tag("/td"),file);
.write(.tag("/tr"),file);
.write(.tag("tr"),file);
.write(.tag("th"),"Number of identified protein :",.tag("/th"),file);
.write(.tag("td"),stat_list[["all_pro_num"]],.tag("/td"),file);
.write(.tag("/tr"),file);
.write(.tag("tr"),file);
.write(.tag("th"),"Number of identified spectra with SAP :",
.tag("/th"),file);
.write(.tag("td"),stat_list[["mut_sp_num"]],.tag("/td"),file);
.write(.tag("/tr"),file);
.write(.tag("tr"),file);
.write(.tag("th"),"Number of identified peptide with SAP :",
.tag("/th"),file);
.write(.tag("td"),stat_list[["mut_pep_num"]],.tag("/td"),file);
.write(.tag("/tr"),file);
.write(.tag("tr"),file);
.write(.tag("th"),"Number of identified protein with SAP :",
.tag("/th"),file);
.write(.tag("td"),stat_list[["mut_pro_num"]],.tag("/td"),file);
.write(.tag("/tr"),file);
.write(.tag("/tbody"),file);
.write(.tag("/table"),.tag("/div"),file);
# .write(.tag("div",class="stat"),file);
# .write(.tag("ul"),file);
# .write(.tag("li"),.tag("b",class="stat_var"),
# "Identified spectrum numbers :",.tag("/b"),
# .blank(4),stat_list[["all_sp_num"]],.tag("/li"),file);
# .write(.tag("li"),.tag("b",class="stat_var"),
# "Identified peptide numbers :",.tag("/b"),.blank(4),
# stat_list[["all_pep_num"]],.tag("/li"),file);
# .write(.tag("li"),.tag("b",class="stat_var"),
# "Identified protein numbers :",.tag("/b"),
# .blank(4),stat_list[["all_pro_num"]],.tag("/li"),file);
# .write(.tag("li"),.tag("b",class="stat_var"),
# "Identified SAPs' peptide numbers :",.tag("/b"),
# .blank(4),stat_list[["mut_pep_num"]],.tag("/li"),file);
# .write(.tag("li"),.tag("b",class="stat_var"),
# "Identified SAPs' protein numbers :",.tag("/b"),
# .blank(4),stat_list[["mut_pro_num"]],.tag("/li"),file);
# .write(.tag("/ul"),file);
# .write(.tag("/div"),file);
.write(.ctag("br"),.ctag("hr",class="clear-contentunit"),.ctag("br"),file);
.write(.tag("h1"),"Summary Chart",.tag("/h1"),.ctag("br"),file);
.write(.tag("div",other='style="text-align:center"'),file);
.write(.tag("h2"),"Precursor error",.tag("/h2"),file);
.write(.ctag("img",other=paste('style="width:520px" src="../',
.DATA.DIR,'/precursor_ms1_error.png"',sep="")),.ctag("br"),file);
.write(.tag("/div"),file);
.write(.ctag("br"),file);
.write(.tag("div",other='style="text-align:center"'),file);
.write(.tag("h2"),"Evalue distribution of wild and mut peptides",
.tag("/h2"),file);
.write(.ctag("img",other=paste('style="width:520px" src="../',.DATA.DIR,
'/wild_mut_evalue_hist.png"',sep="")),.ctag("br"),file);
.write(.tag("/div"),file);
.write(.ctag("br"),file);
.write(.tag("div",other='style="text-align:center"'),file);
.write(.tag("h2"),"Mass distribution of wild and mut peptides",
.tag("/h2"),file);
.write(.ctag("img",other=paste('style="width:520px" src="../',.DATA.DIR,
'/wild_mut_mass_hist.png"',sep="")),.ctag("br"),file);
.write(.tag("/div"),file);
.write(.ctag("br"),file);
.write(.tag("div",other='style="text-align:center"'),file);
.write(.tag("h2"),"Charge distribution of wild and mut peptides",
.tag("/h2"),file);
.write(.ctag("img",other=paste('style="width:520px" src="../',.DATA.DIR,
'/wild_mut_charge_barplot.png"',sep="")),.ctag("br"),file);
.write(.tag("/div"),file);
.write(.ctag("br"),file);
.write(.tag("div",other='style="text-align:center"'),file);
.write(.tag("h2"),"SAP number distribution of each protein",
.tag("/h2"),file);
.write(.ctag("img",other=paste('style="width:520px" src="../',.DATA.DIR,
'/mut_num_each_protein_barplot.png"',sep="")),.ctag("br"),file);
.write(.tag("/div"),file);
.write(.ctag("br"),.ctag("hr",class="clear-contentunit"),
.ctag("br"),file);
.write(.tag("h1"),"Summary Table",.tag("/h1"),.ctag("br"),file);
.write(.tag("div",other='style="text-align:center"'),file);
.write(.tag("/div"),file);
.write(.tag("div"),.tag("table"),file);
.writeTable("Peptide","AA_wild","AA_site","AA_mut","AA_delta(Da)",
"Evalue","SPC","isUnique","isWM","Link",tg1="thead",tg2="th",out=file);
.write(.tag("tbody"),file);
for(p in 1:length(data))
{
if(p %% 2 == 0)
{
color="#F0F0F0";
}
else
{
color="#FFF";
}
for(m in 1:length(data[[p]]))
{
tag_link=.concat(.tag("a",other=.concat('href="',
names(data[p]),'.html"')),data[[p]][[m]][["pro"]],.tag("/a"));
isWM="no";
if(!is.null(wmlist[[ data[[p]][[m]][["pro"]] ]]))
{
tmp<-wmlist[[ data[[p]][[m]][["pro"]] ]]
if(!is.na(tmp[ data[[p]][[m]][["AA_site"]] ]))
{
isWM="yes";
}
}
if(length(data[[p]])==1)
{
highlight_pep<-.mut_highlight(names(data[[p]][m]),
data[[p]][[m]][["rel_coord"]]);
.writeTable(highlight_pep,
data[[p]][[m]][["AA_wild"]],
data[[p]][[m]][["AA_site"]],
data[[p]][[m]][["AA_mut"]],
data[[p]][[m]][["AA_delta"]],
data[[p]][[m]][["evalue"]],
data[[p]][[m]][["spc"]],
data[[p]][[m]][["is_unique"]],
isWM,tag_link,
bg=color,out=file);
}
else
{
if(m==1)
{
highlight_pep<-.mut_highlight(names(data[[p]][m]),
data[[p]][[m]][["rel_coord"]]);
.write(.tag("tr",other=
.concat('style="background:',color,'"')),file);
.write(.tag("td"),highlight_pep,.tag("/td"),file);
.write(.tag("td"),data[[p]][[m]][["AA_wild"]],
.tag("/td"),file);
.write(.tag("td"),data[[p]][[m]][["AA_site"]],
.tag("/td"),file);
.write(.tag("td"),data[[p]][[m]][["AA_mut"]],
.tag("/td"),file);
.write(.tag("td"),data[[p]][[m]][["AA_delta"]],
.tag("/td"),file);
.write(.tag("td"),data[[p]][[m]][["evalue"]],
.tag("/td"),file);
.write(.tag("td"),data[[p]][[m]][["spc"]],
.tag("/td"),file);
.write(.tag("td"),data[[p]][[m]][["is_unique"]],
.tag("/td"),file);
.write(.tag("td"),isWM,.tag("/td"),file);
.write(.tag("td",other=.concat("rowspan=",
length(data[[p]]))),tag_link,.tag("/td"),file);
.write(.tag("/tr"),file);
}
else
{
highlight_pep<-.mut_highlight(names(data[[p]][m]),
data[[p]][[m]][["rel_coord"]]);
.writeTable(highlight_pep,
data[[p]][[m]][["AA_wild"]],
data[[p]][[m]][["AA_site"]],
data[[p]][[m]][["AA_mut"]],
data[[p]][[m]][["AA_delta"]],
data[[p]][[m]][["evalue"]],
data[[p]][[m]][["spc"]],
data[[p]][[m]][["is_unique"]],
isWM,bg=color,out=file);
}
}
}
}
.write(.tag("/tbody"),file);
.write(.tag("/table"),.tag("/div"),file);
.write(.ctag("br"),.ctag("hr",class="clear-contentunit"),
.ctag("br"),file);
.write(.tag("div",class="top_btn"),.tag("/div"),file); #-----.top_btn--->
.write(.tag("/div"),file);
.write(.tag("/body"),file);
}
# .pepsummary
#
# extract the data for peptide table. input is the dobj
#
# @author xsh
.pepsummary<-function(data)
{
pro_pep_pair=c()
for(p in 2:length(data))
{
for(i in 2:length(data[[p]][["IMUT"]]))
{
lines=unlist(strsplit(data[[p]][["IMUT"]][[i]],"\n"));
for(l in lines)
{
arr=unlist(strsplit(l,"\t"));
pro_pep_pair=c(paste(data[[p]][["TRAN"]],
arr[10],sep="\t"),pro_pep_pair);
}
}
}
is_uniq_list=list()
for(p in unique(pro_pep_pair))
{
elem=unlist(strsplit(p,"\t"));
if(!is.null(is_uniq_list[[ elem[2] ]]))
{
is_uniq_list[[ elem[2] ]]="no";
}
else
{
is_uniq_list[[ elem[2] ]]="yes";
}
}
pro_list=list()
for(p in 2:length(data))
{
pro_id=data[[p]][["TRAN"]];
pep_list=list();
for(i in 2:length(data[[p]][["IMUT"]]))
{
#elem=unlist(strsplit(names(data[[p]][["IMUT"]][i]),"\t"));
#wild_aa=elem[2];
#mut_aa=elem[3];
lines=unlist(strsplit(data[[p]][["IMUT"]][[i]],"\n"));
aa_site<-unlist(strsplit(names(data[[p]][["IMUT"]][i]),"\t"))[1];
for(l in lines)
{
arr=unlist(strsplit(l,"\t"));
if(!is.null(pep_list[[ arr[10] ]]))
{
if (pep_list[[ arr[10] ]][["evalue"]]>as.numeric(arr[8]))
pep_list[[ arr[10] ]][["evalue"]]=as.numeric(arr[8]);
pep_list[[ arr[10] ]][["spc"]]=
as.numeric(pep_list[[ arr[10] ]][["spc"]])+1;
}
else
{
pep_list[[ arr[10] ]][["evalue"]]=as.numeric(arr[8]);
pep_list[[ arr[10] ]][["spc"]]=1;
pep_list[[ arr[10] ]][["pro"]]=pro_id;
pep_list[[ arr[10] ]][["AA_wild"]]=arr[12];
pep_list[[ arr[10] ]][["AA_mut"]]=arr[13];
pep_list[[ arr[10] ]][["AA_site"]]=aa_site;
pep_list[[ arr[10] ]][["rel_coord"]]=arr[14];
# tryCatch(
# {
# pep_list[[ arr[10] ]][["AA_delta"]]=
# round(.AA.TABLE[[arr[13]]]-.AA.TABLE[[arr[12]]],
# digits=2)},
# error = function(err)
# paste(err,pro_id,sep=" ")).
if(arr[13] == "*")
{
pep_list[[ arr[10] ]][["AA_delta"]]=
round(-.AA.TABLE[[arr[12]]],digits=2);
}
else if(arr[12]=="*")
{
pep_list[[ arr[10] ]][["AA_delta"]]=
round(.AA.TABLE[[arr[13]]],digits=2);
}
else
{
pep_list[[ arr[10] ]][["AA_delta"]]=
round(.AA.TABLE[[arr[13]]]-.AA.TABLE[[arr[12]]],
digits=2);
}
pep_list[[arr[10]]][["is_unique"]]=is_uniq_list[[arr[10]]];
}
}
}
pro_list[[ names(data[p]) ]]=pep_list;
}
return(pro_list)
}
#############################main###############################
# .rshtml
#
# Creates the html statistics page of identification;
#
# @param data List object from .dataHandle_R
# @param pep.summary.path The peptide summary file.
# @param pro.summary.path The protein summary file.
# @param wmlist The list object from \code{rchtml}
.rshtml<-function(data,pep.summary.path,pro.summary.path,wmlist,outdir)
{
#This is just a mock variable,and it will remove the note(not warning)
#caused by subset;
peptide<-index<-isSAP<-NULL;
page_dir=paste(outdir,.PAGE.DIR,sep="/");
if(!file.exists(page_dir))
{
dir.create(page_dir);
cssdir=paste(system.file(package="sapFinder"),"css",sep="/");
imdir=paste(system.file(package="sapFinder"),"images",sep="/");
jsdir=paste(system.file(package="sapFinder"),"js",sep="/");
file.copy(c(cssdir,imdir,jsdir),page_dir,recursive = TRUE);
}
data_dir=paste(outdir,.DATA.DIR,sep="/");
if(!file.exists(data_dir))
{
dir.create(data_dir);
}
###################1.heatmap##########
#png(paste(.DATA.DIR,"mutation_frequency_heatmap.png",sep="/"),
# width = 520, height = 520)
#.mut_freq_heatmap(map.table)
#dev.off()
pep.df<-read.delim(pep.summary.path,header=TRUE,stringsAsFactors=FALSE);
pro.df<-read.delim(pro.summary.path,header=TRUE,stringsAsFactors=FALSE);
pep.df$delta_ppm=as.numeric(pep.df$delta_ppm);
pep.df$delta_da=as.numeric(pep.df$delta_da);
pep.df$mass=as.numeric(pep.df$mass);
pep.df$evalue=as.numeric(pep.df$evalue);
stat_list<-list();
stat_list[["all_pro_num"]]<-dim(pro.df)[1];
stat_list[["all_sp_num"]]<-dim(pep.df)[1];
stat_list[["all_pep_num"]]<-length(unique(pep.df$peptide));
stat_list[["mut_pep_num"]]<-dim(unique(subset(pep.df,isSAP=="true",
select=c(peptide))))[1];
stat_list[["mut_pro_num"]]<-length(data)-1;
stat_list[["mut_sp_num"]]<-dim(unique(subset(pep.df,isSAP=="true",
select=c(index))))[1];
#mut_num_vector=c()
#for(p in 2:length(data))
#{
# for(i in 2:length(data[[p]][["IMUT"]]))
# {
# tmp=unlist(strsplit(names(data[[p]][["IMUT"]][i]),"\t"))[5];
# mut_num_vector=c(mut_num_vector,unlist(strsplit(tmp,'[|]')));
# }
#}
#mut_num=length(unique(mut_num_vector))
#################2.mass distribution of MS level one ###################
png(paste(data_dir,"precursor_ms1_error.png",sep="/"),
width = 540, height = 420);
par(mar=c(4,4,1,1));
.precursor_error_hist(pep.df);
dev.off();
###########3.Evalue histogram of mutant peptide and wild peptide#########
png(paste(data_dir,"wild_mut_evalue_hist.png",sep="/"),
width = 540, height = 420);
par(mar=c(4, 4, 1, 1));
.wm_evalue_hist(pep.df);
dev.off();
#######4.Mass histogram of mutant peptide and wild peptide###############
png(paste(data_dir,"wild_mut_mass_hist.png",sep="/"),
width = 540, height = 420);
par(mar=c(4, 4, 1, 1));
.wm_mass_hist(pep.df);
dev.off();
#######5.Charge barplot of mutant peptide and wild peptide###############
png(paste(data_dir,"wild_mut_charge_barplot.png",sep="/"),
width = 540, height = 420);
par(mar=c(4,4,1,1));
.wm_charge_bar(pep.df);
dev.off();
#########6.barplot of protein number ##########
png(paste(data_dir,"mut_num_each_protein_barplot.png",sep="/"),
width = 540, height = 420);
par(mar=c(4,4,1,1));
.mut_pro_dist(data);
dev.off();
####### data process
fdata<-.pepsummary(data);
####### writing html
.writeHtml_s(fdata,stat_list,
pep.summary.path,
pro.summary.path,
filename="search_stat",
wmlist=wmlist,
outdir=outdir);
}
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Defines functions .rshtml .pepsummary .writeBody_s .writeHead_s .writeHtml_s
# .writeHtml_s
#
# write the html;
#
# @author xsh
.writeHtml_s<-function(data,stat_list,pep.summary.path,
pro.summary.path,filename="myTest",wmlist,outdir)
{
page_dir=paste(outdir,.PAGE.DIR,sep="/");
filename=.concat(page_dir,"/", filename, ".html" );
file=file(filename,"w");
cat('<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"',
' "http://www.w3.org/TR/html4/loose.dtd">\n', file=file, sep="");
.write(.tag("html"),file);
.writeHead_s(file);
.writeBody_s(data,stat_list,pep.summary.path,pro.summary.path,
file,wmlist=wmlist);
.write(.tag("/html"),file);
close(file);
}
# .writeHead_i
#
# write the header partion;
#
# @author xsh
.writeHead_s<-function(file)
{
.write(.tag("head"),file);
meta<-'http-equiv="Content-Type" content="text/html; charset=utf-8"';
.write(.ctag("meta",other=meta),file);
.write(.tag("title"),"stat",.tag("/title"),file);
.write(.tag("script",
other=paste('type=\"text/javascript\" src=','"',
.JAVASCRIPT.DIR,"/",.JQUERY.MIN.JS,'"',sep="")),nobreak=TRUE, file);
.write( .tag("/script"), file );
.write(.tag("script",
other=paste('type=\"text/javascript\" src=','"',.JAVASCRIPT.DIR,
"/",.INDEX.JS,'"',sep="")),nobreak=TRUE, file);
.write( .tag("/script"), file );
.write(.tag("link",other=paste('rel="stylesheet" type="text/css" href=',
'"',.CSS.DIR,"/",.INDEX.CSS,'"',sep="")),nobreak=TRUE, file);
.write( .tag("/link"), file );
.write(.tag("style",other='type="text/css"'),
"html{overflow:auto;};body{position:relative;}",.tag("/style"),file);
.write(.tag("/head"),file);
}
# .writeBody_g
#
# write the body partion;
#
# @author xsh
.writeBody_s<-function(data,stat_list,
pep.summary.path,
pro.summary.path,
file,wmlist)
{
.write(.tag("body"),file);
.write(.tag("div",class="seq_cn1"),file);
.write(.tag("a",class="button contenttoggle",
other=.concat('title="Click to download" href="../',.DATA.DIR,'/',
basename(pep.summary.path),'"')),"Download peptide summary",
.tag("/a"),file);
.write(.tag("a",class="button contenttoggle",
other=.concat('title="Click to download" href="../',.DATA.DIR,'/',
basename(pro.summary.path),'"')),"Download protide summary",
.tag("/a"),file);
.write(.ctag("br"),.ctag("hr",class="clear-contentunit"),.ctag("br"),file);
.write(.tag("h1"),"Summary List",.tag("/h1"),.ctag("br"),file);
.write(.tag("div"),.tag("table",class="stat"),file);
.write(.tag("tbody"),file);
.write(.tag("tr"),file);
.write(.tag("th"),"Number of identified spectra :",.tag("/th"),file);
.write(.tag("td"),stat_list[["all_sp_num"]],.tag("/td"),file);
.write(.tag("/tr"),file);
.write(.tag("tr"),file);
.write(.tag("th"),"Number of identified peptide :",.tag("/th"),file);
.write(.tag("td"),stat_list[["all_pep_num"]],.tag("/td"),file);
.write(.tag("/tr"),file);
.write(.tag("tr"),file);
.write(.tag("th"),"Number of identified protein :",.tag("/th"),file);
.write(.tag("td"),stat_list[["all_pro_num"]],.tag("/td"),file);
.write(.tag("/tr"),file);
.write(.tag("tr"),file);
.write(.tag("th"),"Number of identified spectra with SAP :",
.tag("/th"),file);
.write(.tag("td"),stat_list[["mut_sp_num"]],.tag("/td"),file);
.write(.tag("/tr"),file);
.write(.tag("tr"),file);
.write(.tag("th"),"Number of identified peptide with SAP :",
.tag("/th"),file);
.write(.tag("td"),stat_list[["mut_pep_num"]],.tag("/td"),file);
.write(.tag("/tr"),file);
.write(.tag("tr"),file);
.write(.tag("th"),"Number of identified protein with SAP :",
.tag("/th"),file);
.write(.tag("td"),stat_list[["mut_pro_num"]],.tag("/td"),file);
.write(.tag("/tr"),file);
.write(.tag("/tbody"),file);
.write(.tag("/table"),.tag("/div"),file);
# .write(.tag("div",class="stat"),file);
# .write(.tag("ul"),file);
# .write(.tag("li"),.tag("b",class="stat_var"),
# "Identified spectrum numbers :",.tag("/b"),
# .blank(4),stat_list[["all_sp_num"]],.tag("/li"),file);
# .write(.tag("li"),.tag("b",class="stat_var"),
# "Identified peptide numbers :",.tag("/b"),.blank(4),
# stat_list[["all_pep_num"]],.tag("/li"),file);
# .write(.tag("li"),.tag("b",class="stat_var"),
# "Identified protein numbers :",.tag("/b"),
# .blank(4),stat_list[["all_pro_num"]],.tag("/li"),file);
# .write(.tag("li"),.tag("b",class="stat_var"),
# "Identified SAPs' peptide numbers :",.tag("/b"),
# .blank(4),stat_list[["mut_pep_num"]],.tag("/li"),file);
# .write(.tag("li"),.tag("b",class="stat_var"),
# "Identified SAPs' protein numbers :",.tag("/b"),
# .blank(4),stat_list[["mut_pro_num"]],.tag("/li"),file);
# .write(.tag("/ul"),file);
# .write(.tag("/div"),file);
.write(.ctag("br"),.ctag("hr",class="clear-contentunit"),.ctag("br"),file);
.write(.tag("h1"),"Summary Chart",.tag("/h1"),.ctag("br"),file);
.write(.tag("div",other='style="text-align:center"'),file);
.write(.tag("h2"),"Precursor error",.tag("/h2"),file);
.write(.ctag("img",other=paste('style="width:520px" src="../',
.DATA.DIR,'/precursor_ms1_error.png"',sep="")),.ctag("br"),file);
.write(.tag("/div"),file);
.write(.ctag("br"),file);
.write(.tag("div",other='style="text-align:center"'),file);
.write(.tag("h2"),"Evalue distribution of wild and mut peptides",
.tag("/h2"),file);
.write(.ctag("img",other=paste('style="width:520px" src="../',.DATA.DIR,
'/wild_mut_evalue_hist.png"',sep="")),.ctag("br"),file);
.write(.tag("/div"),file);
.write(.ctag("br"),file);
.write(.tag("div",other='style="text-align:center"'),file);
.write(.tag("h2"),"Mass distribution of wild and mut peptides",
.tag("/h2"),file);
.write(.ctag("img",other=paste('style="width:520px" src="../',.DATA.DIR,
'/wild_mut_mass_hist.png"',sep="")),.ctag("br"),file);
.write(.tag("/div"),file);
.write(.ctag("br"),file);
.write(.tag("div",other='style="text-align:center"'),file);
.write(.tag("h2"),"Charge distribution of wild and mut peptides",
.tag("/h2"),file);
.write(.ctag("img",other=paste('style="width:520px" src="../',.DATA.DIR,
'/wild_mut_charge_barplot.png"',sep="")),.ctag("br"),file);
.write(.tag("/div"),file);
.write(.ctag("br"),file);
.write(.tag("div",other='style="text-align:center"'),file);
.write(.tag("h2"),"SAP number distribution of each protein",
.tag("/h2"),file);
.write(.ctag("img",other=paste('style="width:520px" src="../',.DATA.DIR,
'/mut_num_each_protein_barplot.png"',sep="")),.ctag("br"),file);
.write(.tag("/div"),file);
.write(.ctag("br"),.ctag("hr",class="clear-contentunit"),
.ctag("br"),file);
.write(.tag("h1"),"Summary Table",.tag("/h1"),.ctag("br"),file);
.write(.tag("div",other='style="text-align:center"'),file);
.write(.tag("/div"),file);
.write(.tag("div"),.tag("table"),file);
.writeTable("Peptide","AA_wild","AA_site","AA_mut","AA_delta(Da)",
"Evalue","SPC","isUnique","isWM","Link",tg1="thead",tg2="th",out=file);
.write(.tag("tbody"),file);
for(p in 1:length(data))
{
if(p %% 2 == 0)
{
color="#F0F0F0";
}
else
{
color="#FFF";
}
for(m in 1:length(data[[p]]))
{
tag_link=.concat(.tag("a",other=.concat('href="',
names(data[p]),'.html"')),data[[p]][[m]][["pro"]],.tag("/a"));
isWM="no";
if(!is.null(wmlist[[ data[[p]][[m]][["pro"]] ]]))
{
tmp<-wmlist[[ data[[p]][[m]][["pro"]] ]]
if(!is.na(tmp[ data[[p]][[m]][["AA_site"]] ]))
{
isWM="yes";
}
}
if(length(data[[p]])==1)
{
highlight_pep<-.mut_highlight(names(data[[p]][m]),
data[[p]][[m]][["rel_coord"]]);
.writeTable(highlight_pep,
data[[p]][[m]][["AA_wild"]],
data[[p]][[m]][["AA_site"]],
data[[p]][[m]][["AA_mut"]],
data[[p]][[m]][["AA_delta"]],
data[[p]][[m]][["evalue"]],
data[[p]][[m]][["spc"]],
data[[p]][[m]][["is_unique"]],
isWM,tag_link,
bg=color,out=file);
}
else
{
if(m==1)
{
highlight_pep<-.mut_highlight(names(data[[p]][m]),
data[[p]][[m]][["rel_coord"]]);
.write(.tag("tr",other=
.concat('style="background:',color,'"')),file);
.write(.tag("td"),highlight_pep,.tag("/td"),file);
.write(.tag("td"),data[[p]][[m]][["AA_wild"]],
.tag("/td"),file);
.write(.tag("td"),data[[p]][[m]][["AA_site"]],
.tag("/td"),file);
.write(.tag("td"),data[[p]][[m]][["AA_mut"]],
.tag("/td"),file);
.write(.tag("td"),data[[p]][[m]][["AA_delta"]],
.tag("/td"),file);
.write(.tag("td"),data[[p]][[m]][["evalue"]],
.tag("/td"),file);
.write(.tag("td"),data[[p]][[m]][["spc"]],
.tag("/td"),file);
.write(.tag("td"),data[[p]][[m]][["is_unique"]],
.tag("/td"),file);
.write(.tag("td"),isWM,.tag("/td"),file);
.write(.tag("td",other=.concat("rowspan=",
length(data[[p]]))),tag_link,.tag("/td"),file);
.write(.tag("/tr"),file);
}
else
{
highlight_pep<-.mut_highlight(names(data[[p]][m]),
data[[p]][[m]][["rel_coord"]]);
.writeTable(highlight_pep,
data[[p]][[m]][["AA_wild"]],
data[[p]][[m]][["AA_site"]],
data[[p]][[m]][["AA_mut"]],
data[[p]][[m]][["AA_delta"]],
data[[p]][[m]][["evalue"]],
data[[p]][[m]][["spc"]],
data[[p]][[m]][["is_unique"]],
isWM,bg=color,out=file);
}
}
}
}
.write(.tag("/tbody"),file);
.write(.tag("/table"),.tag("/div"),file);
.write(.ctag("br"),.ctag("hr",class="clear-contentunit"),
.ctag("br"),file);
.write(.tag("div",class="top_btn"),.tag("/div"),file); #-----.top_btn--->
.write(.tag("/div"),file);
.write(.tag("/body"),file);
}
# .pepsummary
#
# extract the data for peptide table. input is the dobj
#
# @author xsh
.pepsummary<-function(data)
{
pro_pep_pair=c()
for(p in 2:length(data))
{
for(i in 2:length(data[[p]][["IMUT"]]))
{
lines=unlist(strsplit(data[[p]][["IMUT"]][[i]],"\n"));
for(l in lines)
{
arr=unlist(strsplit(l,"\t"));
pro_pep_pair=c(paste(data[[p]][["TRAN"]],
arr[10],sep="\t"),pro_pep_pair);
}
}
}
is_uniq_list=list()
for(p in unique(pro_pep_pair))
{
elem=unlist(strsplit(p,"\t"));
if(!is.null(is_uniq_list[[ elem[2] ]]))
{
is_uniq_list[[ elem[2] ]]="no";
}
else
{
is_uniq_list[[ elem[2] ]]="yes";
}
}
pro_list=list()
for(p in 2:length(data))
{
pro_id=data[[p]][["TRAN"]];
pep_list=list();
for(i in 2:length(data[[p]][["IMUT"]]))
{
#elem=unlist(strsplit(names(data[[p]][["IMUT"]][i]),"\t"));
#wild_aa=elem[2];
#mut_aa=elem[3];
lines=unlist(strsplit(data[[p]][["IMUT"]][[i]],"\n"));
aa_site<-unlist(strsplit(names(data[[p]][["IMUT"]][i]),"\t"))[1];
for(l in lines)
{
arr=unlist(strsplit(l,"\t"));
if(!is.null(pep_list[[ arr[10] ]]))
{
if (pep_list[[ arr[10] ]][["evalue"]]>as.numeric(arr[8]))
pep_list[[ arr[10] ]][["evalue"]]=as.numeric(arr[8]);
pep_list[[ arr[10] ]][["spc"]]=
as.numeric(pep_list[[ arr[10] ]][["spc"]])+1;
}
else
{
pep_list[[ arr[10] ]][["evalue"]]=as.numeric(arr[8]);
pep_list[[ arr[10] ]][["spc"]]=1;
pep_list[[ arr[10] ]][["pro"]]=pro_id;
pep_list[[ arr[10] ]][["AA_wild"]]=arr[12];
pep_list[[ arr[10] ]][["AA_mut"]]=arr[13];
pep_list[[ arr[10] ]][["AA_site"]]=aa_site;
pep_list[[ arr[10] ]][["rel_coord"]]=arr[14];
# tryCatch(
# {
# pep_list[[ arr[10] ]][["AA_delta"]]=
# round(.AA.TABLE[[arr[13]]]-.AA.TABLE[[arr[12]]],
# digits=2)},
# error = function(err)
# paste(err,pro_id,sep=" ")).
if(arr[13] == "*")
{
pep_list[[ arr[10] ]][["AA_delta"]]=
round(-.AA.TABLE[[arr[12]]],digits=2);
}
else if(arr[12]=="*")
{
pep_list[[ arr[10] ]][["AA_delta"]]=
round(.AA.TABLE[[arr[13]]],digits=2);
}
else
{
pep_list[[ arr[10] ]][["AA_delta"]]=
round(.AA.TABLE[[arr[13]]]-.AA.TABLE[[arr[12]]],
digits=2);
}
pep_list[[arr[10]]][["is_unique"]]=is_uniq_list[[arr[10]]];
}
}
}
pro_list[[ names(data[p]) ]]=pep_list;
}
return(pro_list)
}
#############################main###############################
# .rshtml
#
# Creates the html statistics page of identification;
#
# @param data List object from .dataHandle_R
# @param pep.summary.path The peptide summary file.
# @param pro.summary.path The protein summary file.
# @param wmlist The list object from \code{rchtml}
.rshtml<-function(data,pep.summary.path,pro.summary.path,wmlist,outdir)
{
#This is just a mock variable,and it will remove the note(not warning)
#caused by subset;
peptide<-index<-isSAP<-NULL;
page_dir=paste(outdir,.PAGE.DIR,sep="/");
if(!file.exists(page_dir))
{
dir.create(page_dir);
cssdir=paste(system.file(package="sapFinder"),"css",sep="/");
imdir=paste(system.file(package="sapFinder"),"images",sep="/");
jsdir=paste(system.file(package="sapFinder"),"js",sep="/");
file.copy(c(cssdir,imdir,jsdir),page_dir,recursive = TRUE);
}
data_dir=paste(outdir,.DATA.DIR,sep="/");
if(!file.exists(data_dir))
{
dir.create(data_dir);
}
###################1.heatmap##########
#png(paste(.DATA.DIR,"mutation_frequency_heatmap.png",sep="/"),
# width = 520, height = 520)
#.mut_freq_heatmap(map.table)
#dev.off()
pep.df<-read.delim(pep.summary.path,header=TRUE,stringsAsFactors=FALSE);
pro.df<-read.delim(pro.summary.path,header=TRUE,stringsAsFactors=FALSE);
pep.df$delta_ppm=as.numeric(pep.df$delta_ppm);
pep.df$delta_da=as.numeric(pep.df$delta_da);
pep.df$mass=as.numeric(pep.df$mass);
pep.df$evalue=as.numeric(pep.df$evalue);
stat_list<-list();
stat_list[["all_pro_num"]]<-dim(pro.df)[1];
stat_list[["all_sp_num"]]<-dim(pep.df)[1];
stat_list[["all_pep_num"]]<-length(unique(pep.df$peptide));
stat_list[["mut_pep_num"]]<-dim(unique(subset(pep.df,isSAP=="true",
select=c(peptide))))[1];
stat_list[["mut_pro_num"]]<-length(data)-1;
stat_list[["mut_sp_num"]]<-dim(unique(subset(pep.df,isSAP=="true",
select=c(index))))[1];
#mut_num_vector=c()
#for(p in 2:length(data))
#{
# for(i in 2:length(data[[p]][["IMUT"]]))
# {
# tmp=unlist(strsplit(names(data[[p]][["IMUT"]][i]),"\t"))[5];
# mut_num_vector=c(mut_num_vector,unlist(strsplit(tmp,'[|]')));
# }
#}
#mut_num=length(unique(mut_num_vector))
#################2.mass distribution of MS level one ###################
png(paste(data_dir,"precursor_ms1_error.png",sep="/"),
width = 540, height = 420);
par(mar=c(4,4,1,1));
.precursor_error_hist(pep.df);
dev.off();
###########3.Evalue histogram of mutant peptide and wild peptide#########
png(paste(data_dir,"wild_mut_evalue_hist.png",sep="/"),
width = 540, height = 420);
par(mar=c(4, 4, 1, 1));
.wm_evalue_hist(pep.df);
dev.off();
#######4.Mass histogram of mutant peptide and wild peptide###############
png(paste(data_dir,"wild_mut_mass_hist.png",sep="/"),
width = 540, height = 420);
par(mar=c(4, 4, 1, 1));
.wm_mass_hist(pep.df);
dev.off();
#######5.Charge barplot of mutant peptide and wild peptide###############
png(paste(data_dir,"wild_mut_charge_barplot.png",sep="/"),
width = 540, height = 420);
par(mar=c(4,4,1,1));
.wm_charge_bar(pep.df);
dev.off();
#########6.barplot of protein number ##########
png(paste(data_dir,"mut_num_each_protein_barplot.png",sep="/"),
width = 540, height = 420);
par(mar=c(4,4,1,1));
.mut_pro_dist(data);
dev.off();
####### data process
fdata<-.pepsummary(data);
####### writing html
.writeHtml_s(fdata,stat_list,
pep.summary.path,
pro.summary.path,
filename="search_stat",
wmlist=wmlist,
outdir=outdir);
}
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