Nothing
R/rhhtml.r
In sapFinder: A package for variant peptides detection and visualization in shotgun proteomics.
Defines functions
.rhhtml
.writeBody_h
.writeHead_h
.writeHtml_h
# .writeHtml_h
#
# write the html;
#
# @author xsh
.writeHtml_h<-function(outdir,filename="myTest")
{
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_h(file);
.writeBody_h(file);
.write(.tag("/html"),file);
close(file);
}
# .writeHead_h
#
# write the header partion;
#
# @author xsh
.writeHead_h<-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_h
#
# write the body partion;
#
# @author xsh
.writeBody_h<-function(file)
{
.write(.tag("body"),file);
.write(.tag("div",class="seq_cn1"),file);
#.write(.tag("h1"),"Summary List",.tag("/h1"),.ctag("br"),file);
.write(.tag("div",other='style="text-align:center"'),file);
.write(.ctag("img",other=paste('style="width:800px"
src="images/help_images/help1.png"',sep="")),.ctag("br"),file);
.write(.tag("div",id='plaincontent'),file);
.write(.tag("p",class='ident'),"The main page of this report."
,.tag("/p"),file);
.write(.tag("/div"),file);
.write(.ctag("img",other=paste('style="width:650px"
src="images/help_images/help2.png"',sep="")),.ctag("br"),file);
.write(.tag("div",id='plaincontent'),file);
.write(.tag("p",class='ident'),"The description section.",.tag("/p"),file);
.write(.tag("/div"),file);
.write(.ctag("img",other=paste('style="width:800px"
src="images/help_images/help3.png"',sep="")),.ctag("br"),file);
.write(.tag("div",id='plaincontent'),file);
.write(.tag("p",class='ident'),
'The identified SAPs are highlighted in red, and the un-identified
SAPs in gray. Point the SAP with your mouse, the amino acid
substitution will display in a small box. Click the SAP, you can
get more detailed information about the mutation, such as its
chromosome position and the corresponding MS/MS spectra. Only the
identified SAPs have the "MSMS Summary" section, and the labeled
spectra of the peptide with SAP could be viewed by clicking the
first column of "MSMS Summary".'
,.tag("/p"),file);
.write(.tag("/div"),file);
.write(.ctag("img",other=paste('style="width:900px"
src="images/help_images/help4.png"',sep="")),.ctag("br"),file);
.write(.tag("div",id='plaincontent'),file);
.write(.tag("p",class='ident'),
'The "Peptide Summary Report" section provides the whole list of
identified peptides of the corresponding proteins, in which the
column of "isSAP" indicates whether the peptide contains SAP, while
the column of "miss" means the number of missed cleavages in the
peptides.'
,.tag("/p"),file);
.write(.tag("/div"),file);
.write(.ctag("img",other=paste('style="width:600px"
src="images/help_images/help5.png"',sep="")),.ctag("br"),file);
.write(.tag("div",id='plaincontent'),file);
.write(.tag("p",class='ident'),
'This is the spectra of "RLNEGSSAMANG<b><font
color=\'red\'>V</font></b>EEKEPEAPEM".Green fragment labels
represent all possible matches of b ions. Blue fragment labels
represent all possible matches of y ions. And red labels
represent the fragment ions contain the amino acid substitution,
no matter they are b ions or y ions.'
,.tag("/p"),file);
.write(.tag("/div"),file);
.write(.ctag("img",other=paste('style="width:900px"
src="images/help_images/help6.png"',sep="")),.ctag("br"),file);
.write(.tag("div",id='plaincontent'),file);
.write(.tag("p",class='ident'),
"The Search Stat page shows the identification-related
statistical values and diagrams."
,.tag("/p"),file);
.write(.tag("/div"),file);
.write(.ctag("img",other=paste('style="width:800px"
src="images/help_images/help7.png"',sep="")),.ctag("br"),file);
.write(.tag("div",id='plaincontent'),file);
.write(.tag("p",class='ident'),
'In the Search Stat page, there is a "Summary Table" in which
all of the Variant Peptide detected in this workflow are included.
The meanings of each column is as following:'
,.tag("/p"),file);
.write(.tag("p",class='ident'),
'1."AA_wild" column represents the wild-type amino acid.'
,.tag("/p"),file);
.write(.tag("p",class='ident'),
'2."AA_site" column represents the position of the mutation site
in the coding sequence.'
,.tag("/p"),file);
.write(.tag("p",class='ident'),
'3."AA_mut" column represents the variant amino acid.'
,.tag("/p"),file);
.write(.tag("p",class='ident'),
'4."AA_delta (Da)" column represents the mass difference of
variant from wild-type amino acids (AA_mut - AA_wild).'
,.tag("/p"),file);
.write(.tag("p",class='ident'),
'5."Evalue" column represents the maximal E-value of
corresponding peptide.'
,.tag("/p"),file);
.write(.tag("p",class='ident'),
'6."SPC" column represents the spectral counting of each peptide.'
,.tag("/p"),file);
.write(.tag("p",class='ident'),
'7."isUnique" column represents whether the variant peptide is
unique to one particular protein or not.'
,.tag("/p"),file);
.write(.tag("p",class='ident'),
'8."isWM" column represents whether the variant peptide and
corresponding wild-type peptide are both identified or not.'
,.tag("/p"),file);
.write(.tag("/div"),file);
.write(.ctag("img",other=paste('style="width:900px"
src="images/help_images/help8.png"',sep="")),.ctag("br"),file);
.write(.tag("div",id='plaincontent'),file);
.write(.tag("p",class='ident'),
"The Database Stat page shows the database-related statistical
values about SAPs. And the mutation frequency heatmap illustrates
the count of different amino-acid substitutions in the database."
,.tag("/p"),file);
.write(.tag("/div"),file);
.write(.tag("/div"),file);
.write(.tag("div",class="top_btn"),.tag("/div"),file);
.write(.tag("/div"),file);
#--------------.top_btn------------>
.write(.tag("/body"),file);
}
#############################main###############################
# .rhhtml
#
# Creates the html help page;
.rhhtml<-function(outdir)
{
page_dir=paste(outdir,.PAGE.DIR,sep="/");
data_dir=paste(outdir,.DATA.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);
}
if(!file.exists(data_dir))
{
dir.create(data_dir);
}
.writeHtml_h(outdir,filename="help");
}
Try the sapFinder package in your browser
Any scripts or data that you put into this service are public.
sapFinder documentation built on Nov. 8, 2020, 5:59 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions .rhhtml .writeBody_h .writeHead_h .writeHtml_h
# .writeHtml_h
#
# write the html;
#
# @author xsh
.writeHtml_h<-function(outdir,filename="myTest")
{
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_h(file);
.writeBody_h(file);
.write(.tag("/html"),file);
close(file);
}
# .writeHead_h
#
# write the header partion;
#
# @author xsh
.writeHead_h<-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_h
#
# write the body partion;
#
# @author xsh
.writeBody_h<-function(file)
{
.write(.tag("body"),file);
.write(.tag("div",class="seq_cn1"),file);
#.write(.tag("h1"),"Summary List",.tag("/h1"),.ctag("br"),file);
.write(.tag("div",other='style="text-align:center"'),file);
.write(.ctag("img",other=paste('style="width:800px"
src="images/help_images/help1.png"',sep="")),.ctag("br"),file);
.write(.tag("div",id='plaincontent'),file);
.write(.tag("p",class='ident'),"The main page of this report."
,.tag("/p"),file);
.write(.tag("/div"),file);
.write(.ctag("img",other=paste('style="width:650px"
src="images/help_images/help2.png"',sep="")),.ctag("br"),file);
.write(.tag("div",id='plaincontent'),file);
.write(.tag("p",class='ident'),"The description section.",.tag("/p"),file);
.write(.tag("/div"),file);
.write(.ctag("img",other=paste('style="width:800px"
src="images/help_images/help3.png"',sep="")),.ctag("br"),file);
.write(.tag("div",id='plaincontent'),file);
.write(.tag("p",class='ident'),
'The identified SAPs are highlighted in red, and the un-identified
SAPs in gray. Point the SAP with your mouse, the amino acid
substitution will display in a small box. Click the SAP, you can
get more detailed information about the mutation, such as its
chromosome position and the corresponding MS/MS spectra. Only the
identified SAPs have the "MSMS Summary" section, and the labeled
spectra of the peptide with SAP could be viewed by clicking the
first column of "MSMS Summary".'
,.tag("/p"),file);
.write(.tag("/div"),file);
.write(.ctag("img",other=paste('style="width:900px"
src="images/help_images/help4.png"',sep="")),.ctag("br"),file);
.write(.tag("div",id='plaincontent'),file);
.write(.tag("p",class='ident'),
'The "Peptide Summary Report" section provides the whole list of
identified peptides of the corresponding proteins, in which the
column of "isSAP" indicates whether the peptide contains SAP, while
the column of "miss" means the number of missed cleavages in the
peptides.'
,.tag("/p"),file);
.write(.tag("/div"),file);
.write(.ctag("img",other=paste('style="width:600px"
src="images/help_images/help5.png"',sep="")),.ctag("br"),file);
.write(.tag("div",id='plaincontent'),file);
.write(.tag("p",class='ident'),
'This is the spectra of "RLNEGSSAMANG<b><font
color=\'red\'>V</font></b>EEKEPEAPEM".Green fragment labels
represent all possible matches of b ions. Blue fragment labels
represent all possible matches of y ions. And red labels
represent the fragment ions contain the amino acid substitution,
no matter they are b ions or y ions.'
,.tag("/p"),file);
.write(.tag("/div"),file);
.write(.ctag("img",other=paste('style="width:900px"
src="images/help_images/help6.png"',sep="")),.ctag("br"),file);
.write(.tag("div",id='plaincontent'),file);
.write(.tag("p",class='ident'),
"The Search Stat page shows the identification-related
statistical values and diagrams."
,.tag("/p"),file);
.write(.tag("/div"),file);
.write(.ctag("img",other=paste('style="width:800px"
src="images/help_images/help7.png"',sep="")),.ctag("br"),file);
.write(.tag("div",id='plaincontent'),file);
.write(.tag("p",class='ident'),
'In the Search Stat page, there is a "Summary Table" in which
all of the Variant Peptide detected in this workflow are included.
The meanings of each column is as following:'
,.tag("/p"),file);
.write(.tag("p",class='ident'),
'1."AA_wild" column represents the wild-type amino acid.'
,.tag("/p"),file);
.write(.tag("p",class='ident'),
'2."AA_site" column represents the position of the mutation site
in the coding sequence.'
,.tag("/p"),file);
.write(.tag("p",class='ident'),
'3."AA_mut" column represents the variant amino acid.'
,.tag("/p"),file);
.write(.tag("p",class='ident'),
'4."AA_delta (Da)" column represents the mass difference of
variant from wild-type amino acids (AA_mut - AA_wild).'
,.tag("/p"),file);
.write(.tag("p",class='ident'),
'5."Evalue" column represents the maximal E-value of
corresponding peptide.'
,.tag("/p"),file);
.write(.tag("p",class='ident'),
'6."SPC" column represents the spectral counting of each peptide.'
,.tag("/p"),file);
.write(.tag("p",class='ident'),
'7."isUnique" column represents whether the variant peptide is
unique to one particular protein or not.'
,.tag("/p"),file);
.write(.tag("p",class='ident'),
'8."isWM" column represents whether the variant peptide and
corresponding wild-type peptide are both identified or not.'
,.tag("/p"),file);
.write(.tag("/div"),file);
.write(.ctag("img",other=paste('style="width:900px"
src="images/help_images/help8.png"',sep="")),.ctag("br"),file);
.write(.tag("div",id='plaincontent'),file);
.write(.tag("p",class='ident'),
"The Database Stat page shows the database-related statistical
values about SAPs. And the mutation frequency heatmap illustrates
the count of different amino-acid substitutions in the database."
,.tag("/p"),file);
.write(.tag("/div"),file);
.write(.tag("/div"),file);
.write(.tag("div",class="top_btn"),.tag("/div"),file);
.write(.tag("/div"),file);
#--------------.top_btn------------>
.write(.tag("/body"),file);
}
#############################main###############################
# .rhhtml
#
# Creates the html help page;
.rhhtml<-function(outdir)
{
page_dir=paste(outdir,.PAGE.DIR,sep="/");
data_dir=paste(outdir,.DATA.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);
}
if(!file.exists(data_dir))
{
dir.create(data_dir);
}
.writeHtml_h(outdir,filename="help");
}
Try the sapFinder package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.