Merge branch 'devel' into 'master'

Devel

See merge request !4

DESCRIPTION

 Package: shinyscreen
 Title: Pre-screening of Mass Spectrometry Data 
-Version: 0.1
+Version: 0.3
 Author: Todor Kondić
 Maintainer: Todor Kondić <todor.kondic@uni.lu>
 Authors@R: 
-    person(given = "Todor",
-           family = "Kondić",
-           role = c("aut", "cre"),
-           email = "todor.kondic@uni.lu",
-           comment = c(ORCID = "https://orcid.org/0000-0001-6662-4375"))
+    c(person(given = "Todor",
+             family = "Kondić",
+             role = c("aut", "cre"),
+             email = "todor.kondic@uni.lu",
+             comment = c(ORCID = "https://orcid.org/0000-0001-6662-4375")),
+      person(given = "Hiba Mohammed",
+             family = "Taha",
+             role = c("ctb"),
+             email = "hiba.mohammed-taha@ext.uni.lu"),
+      person(given = "Jessy",
+             family = "Krier",
+             role = c("ctb"),
+             email = "jessy.krier@ext.uni.lu"),
+      person(given = "Mira",
+             family = "Narayanan",
+             role = c("ctb"),
+             email = "mira.narayanan@ext.uni.lu"),
+      person(given = "Anjana",
+             family = "Elapavalore",
+             role = c("ctb"),
+             email = "anjana.elapavalore@ext.uni.lu"))	     
 Description: Pre-screening of Mass Spectrometry Data.
 License: Apache License (>= 2.0)
 Encoding: UTF-8

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
-export(mb.do)
-export(mb.prep)
 export(presc.do)
 export(presc.plot)
-export(sw.do)
 export(presc.shiny)

R/run.R

@@ -7,7 +7,6 @@
 ##' @author Todor Kondić
 attch<-function(...) paste(...,sep='')
 
-
 ##' Do the prescreening.
 ##'
 ##' @title Prescreening on bunch of files.
@@ -44,140 +43,3 @@ presc.do<-function(fn_data,fn_cmpd_l,mode,dest=".",proc=F,...) {
     }
 }
 
-
-
-
-##' Performs massbank workflow on multiple mzML files:
-##'
-##'
-##'  1. Create rdir if it does not exist.
-##'
-##'  2. Generate data subdirectories inside `rdir` that will be used to
-##'  keep the processed data belonging to a particular mzML file in
-##'  the fileset.
-##' 
-##'  3. Generate the full RMassBank settings files by merging the
-##'  sections from the `fn_cmpd_list` with the defaults and place those
-##'  new settings files in the appropriate data subdirs.
-##'
-##'  4. Finally perform the spectral workflow on each data file and
-##'  place the results in the data subdirs.
-##' 
-##' @title Perform MassBank Workflow on Multiple Compound Mixtures
-##' @param fn_data List of mzML data filenames to be processed.
-##' @param fn_cmpd_l Compound list.
-##' @param mode as in msmsRead.
-##' @param dest The destination data directory.
-##' @param combine If TRUE, use combineMultiplicies to merge
-##'     workspaces corresponding to different collisional energies.
-##' @param proc Split work between this amount of processes. If FALSE
-##'     (or, 1), run sequential.
-##' @param split This is the last step before combine
-##' @return A named list of msmsWorkspace objects.
-##' @author Todor Kondić
-##' @export
-sw.do <- function(fn_data, fn_cmpd_l, mode, dest=".", combine=F,
-                  proc=F,split=3) {
-    
-    conf(fn_data,fn_cmpd_l,dest)
-    fread <- function(fn_data) {
-        wd <- fn_data2wd(fn_data,dest)
-        reconf(wd)
-        w <- RMassBank::newMsmsWorkspace()
-        RMassBank::msmsRead(w=w,filetable = get_ftable_fn(wd),
-                            mode=mode,readMethod = "mzR")
-    }
-    fwork <- Vectorize(function(w,wd,steps) {
-        archdir <- file.path(wd,"archive")
-        no_drama_mkdir(archdir)
-        fn_arch <- file.path(archdir,"archive")
-        reconf(wd)
-        RMassBank::msmsWorkflow(w=w,mode=mode,steps=steps,archivename = fn_arch)
-    }, vectorize.args = c("w","wd"),SIMPLIFY=F)
-    
-    w <- if (proc) {
-             cl=parallel::makeCluster(proc)
-             parallel::clusterEvalQ(cl,library(shinyscreen))
-             parallel::clusterMap(cl,fread,fn_data)
-         } else {
-             lapply(fn_data,fread)
-         }
-    wd <- fn_data2wd(fn_data,dest)
-    w <- fwork(w,wd,steps=2:split)
-    if (combine) {
-        ## Combined workflow is not based on a single file, but the
-        ## functions that generate config are. Therefore, lets create
-        ## a fake filename.
-        fakefile <- "combine.mzML"
-        cwd <- fn_data2wd(fakefile,dest)
-        xx <- get_stgs_fn(wd[[1]])
-        file.copy(xx,"combine.ini",overwrite = T)
-        # mk_combine_file(get_stgs_fn(wd),"combine.ini")
-        conf(fakefile,fn_cmpd_l,dest)
-        reconf(cwd)
-        w <- list(RMassBank::combineMultiplicities(w))
-        wd <- list(cwd)
-    }
-    w <- fwork(w,wd,steps=(split+1):8)
-    names(w) <- wd
-    w
-}
-
-##' Creates and prepares mbWorkspace objects before the full workflow
-##' is performed on them. In process, create directory `info` as a
-##' subdir of any particular data dir and place the starting info list
-##' there.
-##'
-##' 
-##' @title Prepare mbWorkspace objects
-##' @param w A list of spectral workspace inputs.
-##' @return Named list of prepared mbWorkspace objects.
-##' @author Todor Kondić
-##' @export
-mb.prep<-function(w) {
-    wd <- names(w)
-    fwork <- Vectorize(function(w,wd) {
-        reconf(wd)
-        idir <- gen_info_dir(wd)
-        mb <- RMassBank::newMbWorkspace(w)
-        RMassBank::resetInfolists(mb)
-        RMassBank::mbWorkflow(mb,infolist_path = get_info_fn(wd))
-    },vectorize.args = c("w","wd"))
-
-    mb <- fwork(w,wd)
-    names(mb) <- wd
-    mb
-}
-
-
-##' Perform the Mass Bank workflow on the prepared mbWorkspace
-##' objects. FOR THE RECORD: writing documentation is boring. Anyway,
-##' record results in the info subfolder of each data subdir.
-##'
-##' 
-##' @title Perform the Mass Bank workflow
-##' @param mb The list of prepared mbWorkspace objects.
-##' @param proc Split work between this amount of processes. If FALSE
-##'     (or, 1), run sequential.
-##' @return The named list of processed mbWorkspace objects.
-##' @author Todor Kondić
-##' @export
-mb.do<-function(mb,proc=F) {
-    wd <- names(mb)
-    infodir <- get_info_dir(wd)
-    fwork <- Vectorize(function(mb,id,wd) {
-        reconf(wd)
-        mb <- RMassBank::resetInfolists(mb)
-        mb <- RMassBank::loadInfolists(mb,id)
-        dcur <- setwd(id)
-        mb <- RMassBank::mbWorkflow(mb,step=1:8)
-        setwd(dcur)
-        mb},vectorize.args = c("mb","id","wd"))
-    if (proc) {
-        cl<-parallel::makeCluster(proc)
-        parallel::clusterEvalQ(cl,library("shinyscreen"))
-        parallel::clusterMap(cl,fwork,mb,infodir,wd)
-    } else {
-        fwork(mb,infodir,wd)
-    }
-}

man/mb.do.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/run.R
-\name{mb.do}
-\alias{mb.do}
-\title{Perform the Mass Bank workflow}
-\usage{
-mb.do(mb, proc = F)
-}
-\arguments{
-\item{mb}{The list of prepared mbWorkspace objects.}
-
-\item{proc}{Split work between this amount of processes. If FALSE
-(or, 1), run sequential.}
-}
-\value{
-The named list of processed mbWorkspace objects.
-}
-\description{
-Perform the Mass Bank workflow on the prepared mbWorkspace
-objects. FOR THE RECORD: writing documentation is boring. Anyway,
-record results in the info subfolder of each data subdir.
-}
-\author{
-Todor Kondić
-}

man/mb.p.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{mb.p}
-\alias{mb.p}
-\title{Parallel Mass Bank Workflow}
-\usage{
-mb.p(mb, infodir, fn_stgs, cl = F)
-}
-\arguments{
-\item{mb}{List of mass bank workflow objects}
-
-\item{infodir}{List of subdirs containing info lists.}
-
-\item{fn_stgs}{List of settings files.}
-
-\item{cl}{Cluster.}
-}
-\value{
-A named list of mbWorkspace objects. The names are derived
-from the input mb sequence.
-}
-\description{
-Interface to parallelised Mass Bank workflow.
-}
-\author{
-Todor Kondić
-}

man/mb.prep.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/run.R
-\name{mb.prep}
-\alias{mb.prep}
-\title{Prepare mbWorkspace objects}
-\usage{
-mb.prep(w)
-}
-\arguments{
-\item{w}{A list of spectral workspace inputs.}
-}
-\value{
-Named list of prepared mbWorkspace objects.
-}
-\description{
-Creates and prepares mbWorkspace objects before the full workflow
-is performed on them. In process, create directory \code{info} as a
-subdir of any particular data dir and place the starting info list
-there.
-}
-\author{
-Todor Kondić
-}

man/mb.v.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{mb.v}
-\alias{mb.v}
-\title{Vectorised Mass Bank Workflow}
-\usage{
-mb.v(mb, infodir, fn_stgs)
-}
-\arguments{
-\item{mb}{List of mass bank workflow objects}
-
-\item{infodir}{List of subdirs containing info lists.}
-
-\item{fn_stgs}{List of settings files.}
-}
-\value{
-A named list of mbWorkspace objects. The names are derived
-from the input mb sequence.
-}
-\description{
-Interface to vectorised Mass Bank workflow.
-}
-\author{
-Todor Kondić
-}

man/presc.plot.Rd

@@ -4,16 +4,18 @@
 \alias{presc.plot}
 \title{Plot the Output of Prescreen}
 \usage{
-presc.plot(wd, mode, out = "prescreen.pdf", pal = "Dark2",
-  cex = 0.75, rt_digits = 2, m_digits = 4)
+presc.plot(prescdf, mode, out = "prescreen.pdf", fn_cmpd_l,
+  pal = "Dark2", cex = 0.75, rt_digits = 2, m_digits = 4)
 }
 \arguments{
-\item{wd}{Sequence of data dirs containing the prescreen subdir.}
+\item{prescdf}{File table data-frame. See presc.shiny for details.}
 
 \item{mode}{RMB mode.}
 
 \item{out}{The name of the output file.}
 
+\item{fn_cmpd_l}{The compound list name.}
+
 \item{pal}{ColorBrewer palette name.}
 
 \item{cex}{As in legend.}
@@ -22,6 +24,8 @@ presc.plot(wd, mode, out = "prescreen.pdf", pal = "Dark2",
 
 \item{m_digits}{Number of digits after the point for the mass.}
 
+\item{wd}{Sequence of data dirs containing the prescreen subdir.}
+
 \item{digits}{Number of significant digits for peak ret times.}
 }
 \value{
@@ -32,4 +36,8 @@ Plot the output of prescreen.
 }
 \author{
 Todor Kondić
+
+Mira Narayanan
+
+Anjana Elapavalore
 }

man/presc.shiny.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mix.R
+\name{presc.shiny}
+\alias{presc.shiny}
+\title{Prescreening with Shiny}
+\usage{
+presc.shiny(prescdf, mode, fn_cmpd_l, pal = "Dark2", cex = 0.75,
+  rt_digits = 2, m_digits = 4)
+}
+\arguments{
+\item{prescdf}{File table data-frame. Columns: Files,ID,wd,tag,set_name ...}
+
+\item{mode}{RMassBank mode.}
+
+\item{fn_cmpd_l}{Compound list file name.}
+
+\item{pal}{ColorBrewer palette.}
+
+\item{cex}{Size of fonts.}
+
+\item{rt_digits}{Number of decimal places for the retention time.}
+
+\item{m_digits}{Number of decimal places for the mass.}
+}
+\value{
+Nothing useful.
+}
+\description{
+Prescreening using shiny interface.
+}
+\author{
+Jessy Krier
+
+Mira Narayanan
+
+Hiba Mohammed Taha
+
+Anjana Elapavalore
+
+Todor Kondić
+}

man/rendersmiles2.Rd

@@ -4,11 +4,13 @@
 \alias{rendersmiles2}
 \title{Turn SMILES to an Image Using Online Resource}
 \usage{
-rendersmiles2(smiles, ...)
+rendersmiles2(smiles, style = "cow", ...)
 }
 \arguments{
 \item{smiles}{The SMILES string.}
 
+\item{style}{Structure style.}
+
 \item{...}{Hand over to renderurl.}
 }
 \value{

man/sw.do.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/run.R
-\name{sw.do}
-\alias{sw.do}
-\title{Perform MassBank Workflow on Multiple Compound Mixtures}
-\usage{
-sw.do(fn_data, fn_cmpd_l, mode, dest = ".", combine = F, proc = F,
-  split = 3)
-}
-\arguments{
-\item{fn_data}{List of mzML data filenames to be processed.}
-
-\item{fn_cmpd_l}{Compound list.}
-
-\item{mode}{as in msmsRead.}
-
-\item{dest}{The destination data directory.}
-
-\item{combine}{If TRUE, use combineMultiplicies to merge
-workspaces corresponding to different collisional energies.}
-
-\item{proc}{Split work between this amount of processes. If FALSE
-(or, 1), run sequential.}
-
-\item{split}{This is the last step before combine}
-}
-\value{
-A named list of msmsWorkspace objects.
-}
-\description{
-Performs massbank workflow on multiple mzML files:
-}
-\details{
-\enumerate{
-\item Create rdir if it does not exist.
-\item Generate data subdirectories inside \code{rdir} that will be used to
-keep the processed data belonging to a particular mzML file in
-the fileset.
-\item Generate the full RMassBank settings files by merging the
-sections from the \code{fn_cmpd_list} with the defaults and place those
-new settings files in the appropriate data subdirs.
-\item Finally perform the spectral workflow on each data file and
-place the results in the data subdirs.
-}
-}
-\author{
-Todor Kondić
-}