cpanse / protviz

Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

protViz - Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

Documentation

The package ships with two pdf vignettes.

browseVignettes('protViz')

vignette('protViz')
vignette('PTM_MarkerFinder')

Installation

CRAN

install.packages('protViz')

from github

install the latest development version

install.packages('devtools')
library(devtools)
install_git('https://github.com/cpanse/protViz', build_vignettes = FALSE, quiet = FALSE)
library(protViz)

or

BiocManager::install('cpanse/protViz')

R CMD build hints

Rcpp::compileAttributes()

tools::package_native_routine_registration_skeleton(".", character_only = FALSE)


RcppExport SEXP _rcpp_module_boot_MyModule();

static const R_CallMethodDef CallEntries[] = {
    {"_rcpp_module_boot_MyModule", (DL_FUNC) &_rcpp_module_boot_MyModule, 0},
    {NULL, NULL, 0}
};

RcppExport void R_init_minModuleEx(DllInfo *dll) {
    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
    R_useDynamicSymbols(dll, FALSE);
}

Docker

docker pull cpanse/protviz \
&& docker run -d -p 8792:8787 cpanse/protviz     

connect to http://yourdockerhost:8791 using a web browser

• username: rstudio
• password: rstudio

Documentation

The package ships with a package vignette (browseVignettes('protViz') and a reference manual (just type ?protViz on the R shell).

Both documents are also available on the package's CRAN page.

Related approaches

• RforProteomics
• Spectra

protviz's Issues

replace pkg RUnit by testthat

remove deisotoper code

to be replaced by R package https://CRAN.R-project.org/package=deisotoper

add decoy string parameter

https://github.com/protViz/protViz/blob/48e048f43e41cad3e6002172318bea5f205c67bb/R/comet.R#L28

Documented arguments not in \usage in documentation object 'PTM_MarkerFinder':

Dear maintainer,

Please see the problems shown on
<https://cran.r-project.org/web/checks/check_results_protViz.html>.

Specifically, see the warnings about 'Documented arguments not in
\usage' in the r-devel checks.  These are from a recent bug fix
(PR#16223, see
<https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16223>): can you
please fix your man pages as necessary?  (In most cases, remove the
documentation for argument '...'.)

Please correct before 2020-02-17 to safely retain your package on CRAN.

Best,
-k

discrepancy between R and awk fdr code snippets

protViz/R/comet.R

Line 9 in 66e5281

summary.cometdecoy <- function(object, psmFdrCutoff=0.05, decoyPattern="^REV_", ...){

contradiction to the following bash code;

#!/bin/bash
  
# scp r28:/scratch/cpanse/downsizingDBs/comet/all2/20201022_002_S223359_474-B4.comet.txt .
COMET="20201022_002_S223359_474-B4.comet.txt"

cat ${COMET} \
  | awk 'NF>16{print}' \
  | awk '$2==1{print}' \
  | sort -n -r -k10 \
  | awk 'BEGIN{dc=0}$16~/^REV_/{dc++}{fdr=dc/(NR-dc);print dc"\t"NR"\t"fdr}'  | less

add 2+ example in man page

ION2C <- function(b, y){
    Hydrogen <- 1.007825
    Oxygen <- 15.994915
    Nitrogen <- 14.003074

    #yo <- fi$y - Oxygen - Hydrogen - Hydrogen
    c <- b + (Nitrogen + (3 * Hydrogen))
    z <- y - (Nitrogen + (3 * Hydrogen))
    
    b2 <- (b + Hydrogen) / 2
    y2 <- (y + Hydrogen) / 2

    return(cbind(b, y, b2 ,y2))
}

decoy comet - replace evalue by sp score

clang 17 warnings

• installing source package ‘protViz’ ...
  ** package ‘protViz’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  using C compiler: ‘clang version 17.0.5’
  using C++ compiler: ‘clang version 17.0.5’
  make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/protViz/src'
  /usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang17/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c protViz_init.c -o protViz_init.o
  /usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang17/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c deisotoper.cpp -o deisotoper.o
  In file included from deisotoper.cpp:1:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:128:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/routines.h:26:
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
  53 | Rprintf("%.*s", num, s);
  | ~~^~ ~~~
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
  57 | REprintf("%.*s", num, s);
  | ~~^~ ~~~
  In file included from deisotoper.cpp:1:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:181:
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  30 | Rf_warningcall(call, s.c_str());
  | ^~~~~~~~~
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this
  30 | Rf_warningcall(call, s.c_str());
  | ^
  | "%s",
  /usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang17/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c aa2mass.cpp -o aa2mass.o
  deisotoper.cpp:14:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  14 | ::Rf_warning(s.c_str());
  | ^~~~~~~~~
  deisotoper.cpp:14:15: note: treat the string as an argument to avoid this
  14 | ::Rf_warning(s.c_str());
  | ^
  | "%s",
  In file included from aa2mass.cpp:32:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:128:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/routines.h:26:
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
  53 | Rprintf("%.*s", num, s);
  | ~~^~ ~~~
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
  57 | REprintf("%.*s", num, s);
  | ~~^~ ~~~
  In file included from aa2mass.cpp:32:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:181:
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  30 | Rf_warningcall(call, s.c_str());
  | ^~~~~~~~~
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this
  30 | Rf_warningcall(call, s.c_str());
  | ^
  | "%s",
  4 warnings generated.
  /usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang17/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c findNN_.cpp -o findNN_.o
  /usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang17/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c computeFragmentIons.c -o computeFragmentIons.o
  In file included from findNN_.cpp:4:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:128:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/routines.h:26:
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
  53 | Rprintf("%.*s", num, s);
  | ~~^~ ~~~
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
  57 | REprintf("%.*s", num, s);
  | ~~^~ ~~~
  In file included from findNN_.cpp:4:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:181:
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  30 | Rf_warningcall(call, s.c_str());
  | ^~~~~~~~~
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this
  30 | Rf_warningcall(call, s.c_str());
  | ^
  | "%s",
  /usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang17/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c computeParentIonMass.c -o computeParentIonMass.o
  3 warnings generated.
  /usr/local/clang17/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang17/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c findNN.c -o findNN.o
  /usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang17/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o
  /usr/local/clang17/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang17/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c fasta.cpp -o fasta.o
  In file included from RcppExports.cpp:4:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:128:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/routines.h:26:
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
  53 | Rprintf("%.*s", num, s);
  | ~~^~ ~~~
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
  57 | REprintf("%.*s", num, s);
  | ~~^~ ~~~
  In file included from RcppExports.cpp:4:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:181:
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  30 | Rf_warningcall(call, s.c_str());
  | ^~~~~~~~~
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this
  30 | Rf_warningcall(call, s.c_str());
  | ^
  | "%s",
  In file included from fasta.cpp:10:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:128:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/routines.h:26:
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
  53 | Rprintf("%.*s", num, s);
  | ~~^~ ~~~
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat]
  57 | REprintf("%.*s", num, s);
  | ~~^~ ~~~
  In file included from fasta.cpp:10:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27:
  In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:181:
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  30 | Rf_warningcall(call, s.c_str());
  | ^~~~~~~~~
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this
  30 | Rf_warningcall(call, s.c_str());
  | ^
  | "%s",
  3 warnings generated.
  3 warnings generated.
  3 warnings generated.
  /usr/local/clang17/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang17/lib -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o protViz.so protViz_init.o deisotoper.o aa2mass.o findNN_.o computeFragmentIons.o computeParentIonMass.o findNN.o RcppExports.o fasta.o
  make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/protViz/src'
  make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/protViz/src'
  make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/protViz/src'
  installing to /data/gannet/ripley/R/packages/tests-clang/protViz.Rcheck/00LOCK-protViz/00new/protViz/libs
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** demo
  ** exec
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded from temporary location
  ** checking absolute paths in shared objects and dynamic libraries
  ** testing if installed package can be loaded from final location
  ** testing if installed package keeps a record of temporary installation path
• DONE (protViz)

add formular in docu C_term + N_term + Hydrogen - Electron;

https://github.com/protViz/protViz/blob/ebd3232ee4bf8415d8468b60ee59d66ee64b7cb1/man/parentIonMass.Rd#L11

C_term + N_term + Hydrogen - Electron;

clang 16

clang 16 is being prepared for release in early March, so it is time to start reporting its issues. See
https://www.stats.ox.ac.uk/pub/bdr/clang16/
including its README.txt

ASMap GenSA RCPmod RMixtCompIO RSQLite RSiena Rbeast Rfast Rvcg TiPS arrow duckdb gmp httpuv mapdeck mcemGLM phyclust protViz rgeoda riot sfheaders stan4bart survival tgstat

RSQLite includes Boost headers and these are too old (1.81 is needed). Please use BH instead, for which an update is being processed and was used for these checks.

Shortly these logs will appear as 'clang16' additional issues.

Please correct before 2023-02-16 to safely retain your package on CRAN. (Some have much closer deadlines for other issues.)

--
Brian D. Ripley, [email protected]
Emeritus Professor of Applied Statistics, University of Oxford

use roxygen2

fragmentIon() for modfied sequences

Hello,

Is their a way to generate fragment ions of a modified sequence using the fragmentIon function.

like:
K[28.02]SKRPK[14.01]SST

Thank you.

new by labeling using legend with fragment ion ordered by m/z values

remove Rcpp:::CxxFlags and Rcpp:::LdFlags() in Makevar

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Subject: CRAN packages using Rcpp:::CxxFlags
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For years the recommended way to link to Rcpp has been

LinkingTo: Rcpp

in the DESCRIPTION file, and using Rcpp:::CxxFlags has been unnecessary. 
Yet packages

     ALKr Langevin PAC Rsomoclu bfp climdex.pcic dynsbm geiger protViz

still do so.  Please remove it, and any use of Rcpp:::LdFlags().

Please do so before Jan 16 to safely retain the package on CRAN.

-- 
Brian D. Ripley,                  [email protected]
Emeritus Professor of Applied Statistics, University of Oxford

`stringsAsFactors = FALSE` - upcoming R 4.0.0.

Dear maintainer,

Please see the problems shown on
<https://cran.r-project.org/web/checks/check_results_protViz.html
<img width="812" alt="Screenshot 2020-02-28 at 09 54 43" src="https://user-images.githubusercontent.com/4901987/75525650-7fe65700-5a10-11ea-850f-fea6a368e608.png">
>.

Specifically, see the problems shown for the r-devel Debian checks.

These can be reproduced by checking with --as-cran using a very current
r-devel (r77865 or later), which makes data.frame() and read.table() use
a stringsAsFactors = FALSE default, which is planned to become the new
default for the upcoming R 4.0.0.

Please see
<https://developer.r-project.org/Blog/public/2020/02/16/stringsasfactors/index.html>
for more information about this change.

Can you please fix your package to work with both the old and new
default?  In principle, this can easily be achieved by adding
stringsAsFactors = TRUE to the relevant calls to data.frame() or
read.table() [or other read.* function calling read.table()], but please
only do this if the sort order used in the string to factor conversion
really does not matter (see the blog post about the locale dependence of
the conversion).  Otherwise, please change to create the factors with
explicitly given levels.

The new problems may be from code in a package you depend on: in this
case, please let me know, and get in touch with the maintainer of that
package.

Please correct before 2020-03-20 to safely retain your package on CRAN.

Best,
-k

template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated

protViz/src/findNN_.cpp

Line 51 in e4a1f7d

class MyComparator : public std::binary_function<double, double, bool> {

Dear maintainer,

Please see the problems shown on
https://cran.r-project.org/web/checks/check_results_protViz.html.

Specifically, please see the installation warnings for
r-devel-linux-x86_64-debian-gcc: these can be reproduced by using a
current snapshot of the GCC 12 toolchain.

GCC 12 adds new warnings for use of C++ standard library features that
are deprecated (or no longer present at all) in recent C++ standards,
including std::unary_function and std::binary_function.

See "C++ Standard Library deprecations" in
https://gcc.gnu.org/gcc-12/porting_to.html for more information.

Can you please fix as necessary?

Please correct before 2022-03-29 to safely retain your package on CRAN.

Best,
-k

Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

checking compiled code ... NOTE
File ‘protViz/libs/protViz.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.

FASTA

add FASTA functions / class

• is.FASTA
• as.FASTA
• read.FASTA
• summary.FASTA
• fcat.FASTA
• tryptic_digest.FASTA