Merge branch 'dev' into 'master'

Dev

See merge request eci/rmb-mix-method!12

DESCRIPTION

@@ -19,10 +19,12 @@ Roxygen: list(markdown = TRUE)
 Collate:
     'mix.R'
     'run.R'
-Imports: 
+Depends:
     RMassBank,
+    RChemMass
+Imports: 
     parallel,
     yaml,
     mzR,
     RColorBrewer,
-    RChemMass
+    curl

R/mix.R

@@ -315,6 +315,51 @@ RMB_EIC_prescreen_df <- function (wd, RMB_mode, FileList, cmpd_list,
               row.names = F)
 }
 
+##' Helper function for rendersmiles2
+##'
+##' @title Render Compound from an Online Resource
+##' @param depictURL The URL of the object to plot.
+##' @param coords The positioning of the image (in data coords).
+##' @param filename Temp filename.
+##' @return Nothing useful.
+##' @author Todor Kondić
+renderurl <- function(depictURL,coords=c(0,0,100,100), filename=tempfile(fileext=".svg")) {
+    h <- new_handle()
+    curl::handle_setopt(h, ssl_verifyhost = 0, ssl_verifypeer=0)
+    curl::curl_download(url=depictURL,filename,handle=h)
+    img <- rsvg(filename)
+    if (length(img)>2) {
+        rasterImage(img,xleft=coords[1],ybottom=coords[2],xright=coords[3],ytop=coords[4])
+    }
+}
+
+
+## rendersmiles <- function(smiles, kekulise=TRUE, coords=c(0,0,100,100), width=200, height=200,
+##                               zoom=1.3,style="cow", annotate="off", abbr="on",suppressh=TRUE,
+##                               showTitle=FALSE, smaLimit=100, sma=NULL) {
+##   dep <- get.depictor(width = width, height = height, zoom = zoom, style = style, annotate = annotate,
+##                       abbr = abbr, suppressh = suppressh, showTitle = showTitle, smaLimit = smaLimit,
+##                       sma = NULL)
+##   library(rcdk)
+##   library(RChemMass)
+##   mol <- getMolecule(smiles)
+##   img <- view.image.2d(mol, depictor=dep)
+##   rasterImage(img, coords[1],coords[2], coords[3],coords[4])
+
+## }
+
+##' Render smiles from an online resource.
+##'
+##' @title Turn SMILES to an Image Using Online Resource
+##' @param smiles The SMILES string.
+##' @param ... Hand over to renderurl.
+##' @return Nothing useful.
+##' @author Todor Kondić
+rendersmiles2 <- function(smiles,...) {
+    dpurl <- buildCDKdepictURL(smiles)
+    renderurl(dpurl,filename=tempfile(fileext=".svg"),...)
+}
+
 ##' Plot the output of prescreen.
 ##'
 ##' @title Plot the Output of Prescreen
@@ -339,16 +384,16 @@ presc.plot <- function(wd,mode,out="prescreen.pdf",pal="Dark2",cex=0.75,rt_digit
 
     wd1 <- wd[[1]]
     df <- read.csv(file=get_cmpd_l_fn(wd1),stringsAsFactors = F)
-    smiles <- df$SMILES
-    no_cmpds <- length(smiles)
+    osmesi <- df$SMILES
+    no_cmpds <- length(osmesi)
     # reconf(wd1)
-    masses <- lapply(smiles,function (smile) {
-        #smiles <- tryCatch(RMassBank::findSmiles(i), error = function(e) NA)
+    masses <- lapply(osmesi,function (smile) {
+        #osmesi <- tryCatch(RMassBank::findSmiles(i), error = function(e) NA)
         zz <- RChemMass::getSuspectFormulaMass(smile)
         zz[[modemap[[mode]]]]
     })
     #message("Masses:",masses)
-    #return(masses)
+    # return(osmesi)
 
     ## Get the basenames of eic files.
     eics <- list.files(path=dfdir[[1]],patt=".*eic.csv")
@@ -389,19 +434,28 @@ presc.plot <- function(wd,mode,out="prescreen.pdf",pal="Dark2",cex=0.75,rt_digit
 
         
         
-        rt_rng <- 1.1*range(sapply(dfs,function(x) x$rt))
-        int_rng <- 1.3*range(sapply(append(dfs_kids,dfs),function(x) x$intensity))
+        rt_rng <- 1.2*range(sapply(dfs,function(x) x$rt))
+        int_rng <- 1.4*range(sapply(append(dfs_kids,dfs),function(x) x$intensity))
         plot.window(rt_rng,int_rng)
         box()
         cols <- RColorBrewer::brewer.pal(n=length(dfs),name=pal)
         lgnd <- Map(function(k,v) paste(k,"= ",formatC(v,format="f",digits=rt_digits),sep=''),symbs,rt_max)
         linfo <- legend("topleft",horiz=T,legend=lbls,col=cols,fill=cols,bty="n",cex=cex)
         legend(x=linfo$rect$left,y=linfo$rect$top-0.5*linfo$rect$h,horiz=T,legend=lgnd,fill=cols,bty="n",cex=cex)
-        text(x=rt_rng[[2]],y=0.5*int_rng[[2]],smiles[[i]],cex=cex,srt=90)
-        x1=1.1*linfo$rect$left
-        y2=0.9*linfo$rect$top
-        x2=1.1*x1
-        y1=0.9*y2
+        #text(x=rt_rng[[2]],y=0.5*int_rng[[2]],osmesi[[i]],cex=cex,srt=90)
+        fxmin=rt_rng[1]+0.75*(rt_rng[2]-rt_rng[1])
+        fxmax=fxmin+0.3*(rt_rng[2]-rt_rng[1])
+        fymin=int_rng[1]+0.6*(int_rng[2]-int_rng[1])
+        fymax=fymin+0.3*(int_rng[2]-int_rng[1])
+
+        xcmp=c(fxmin,fxmax)
+        ycmp=c(fymin,fymax)
+        #xcmp=c(0.99*rt_rng[[1]],rt_rng[[2]])
+
+                                        #ycmp=c(0.99*int_rng[[1]],int_rng[[2]])
+        rendersmiles2(osmesi[i],coords=c(xcmp[1],ycmp[1],xcmp[2],ycmp[2]))
+        # RChemMass::renderSMILES.rcdk(osmesi[i],coords=c(xcmp[[1]],ycmp[[1]],xcmp[[2]],ycmp[[2]]),width=xcmp[[2]]-xcmp[[1]],height=ycmp[[2]]-ycmp[[1]])
+
         cols_kids <- cols[indkids]
         lgnd_kids <- Map(function(k,v) paste(k,"= ",formatC(v,digits=rt_digits,format="f"),sep=''),symbs_kids,rt_max_kids)
         if (length(lgnd_kids)>0) legend(x="bottomleft",horiz=T,legend=lgnd_kids,fill=cols[indkids],bty="n",cex=cex)

README.org

@@ -14,7 +14,7 @@
    2. Plot,
       #+BEGIN_SRC R
       require(rmbmix)
-      presc.plot(list.files(".",patt="2.*POS",include.dirs=T),cex=0.7,digits=4)
+      presc.plot(list.files(".",patt="2.*POS",include.dirs=T),mode="pH",cex=0.7,rt_digits=2,m_digits=4,pal="Dark2",out="prescreen.pdf")
       #+END_SRC
       The only argument is a sequence of absolute paths to directories
       containing the prescreen data. The resulting plot file is going

man/RMB_EIC_prescreen_intrn.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{RMB_EIC_prescreen_intrn}
-\alias{RMB_EIC_prescreen_intrn}
-\title{Prescreen}
-\usage{
-RMB_EIC_prescreen_intrn(archive_name, RMB_mode, FileList, cmpd_list,
-  ppm_limit_fine = 10, EIC_limit = 0.001)
-}
-\arguments{
-\item{archive_name}{...}
-
-\item{RMB_mode}{...}
-
-\item{FileList}{...}
-
-\item{cmpd_list}{...}
-
-\item{ppm_limit_fine}{...}
-
-\item{EIC_limit}{...}
-}
-\description{
-Prescreens. Ripped off from ReSOLUTION
-}
-\author{
-Emma Schymanski, Todor Kondić
-}

man/presc.plot.Rd

@@ -4,18 +4,24 @@
 \alias{presc.plot}
 \title{Plot the Output of Prescreen}
 \usage{
-presc.plot(wd, out = "prescreen.pdf", pal = "Dark2", cex = 0.75,
-  digits = 6)
+presc.plot(wd, mode, out = "prescreen.pdf", pal = "Dark2",
+  cex = 0.75, rt_digits = 2, m_digits = 4)
 }
 \arguments{
 \item{wd}{Sequence of data dirs containing the prescreen subdir.}
 
+\item{mode}{RMB mode.}
+
 \item{out}{The name of the output file.}
 
 \item{pal}{ColorBrewer palette name.}
 
 \item{cex}{As in legend.}
 
+\item{rt_digits}{Number of digits after the point for the retention time.}
+
+\item{m_digits}{Number of digits after the point for the mass.}
+
 \item{digits}{Number of significant digits for peak ret times.}
 }
 \value{

man/presc.single.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{presc.single}
-\alias{presc.single}
-\title{Wrapper for RMB_EIC_Prescreen}
-\usage{
-presc.single(fn_data, stgs_alist, wd, mode, fn_cmpd_l, ppm_lim_fine = 10,
-  EIC_limit = 0.001)
-}
-\arguments{
-\item{fn_data}{The mzML filename.}
-
-\item{stgs_alist}{Settings named list, or a settings filename.}
-
-\item{wd}{Directory under which results are archived.}
-
-\item{mode}{RMB mode.}
-
-\item{fn_cmpd_l}{Filename of the compound list.}
-
-\item{ppm_lim_fine}{The ppm_limit_fine argument to RMB_EIC_Prescreen}
-
-\item{EIC_limit}{Passed down to RMB_EIC_Prescreen.}
-}
-\value{
-result of RMB_EIC_Prescreen
-}
-\description{
-Wrapper for a single prescreening call. Produces output in the
-usual mix method places.
-}
-\author{
-Todor Kondić
-}

man/presc.v.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{presc.v}
-\alias{presc.v}
-\title{Vectorises presc.single}
-\usage{
-presc.v(fn_data, fn_cmpd_l, mode, ppm_lim_fine = 10, EIC_limit = 0.001)
-}
-\arguments{
-\item{fn_data}{Sequence of mzML filenames.}
-
-\item{fn_cmpd_l}{Compound list filename.}
-
-\item{mode}{RMB mode.}
-
-\item{ppm_lim_fine}{Prescreen fine limit (see ReSOLUTION prescreening function).}
-
-\item{EIC_limit}{Prescreen EIC limit (see ReSOLUTION prescreening function).}
-}
-\value{
-Nothing useful.
-}
-\description{
-Vectorises presc.single.
-}
-\author{
-Todor Kondić
-}

man/gen_file_table.Rd → man/rendersmiles2.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/mix.R
-\name{gen_file_table}
-\alias{gen_file_table}
-\title{Generate and Load the RMassBank Settings File}
+\name{rendersmiles2}
+\alias{rendersmiles2}
+\title{Turn SMILES to an Image Using Online Resource}
 \usage{
-gen_file_table(fn_data, n_cmpd, wd)
+rendersmiles2(smiles, ...)
 }
 \arguments{
-\item{fn_data}{The mzML filename.}
+\item{smiles}{The SMILES string.}
 
-\item{n_cmpd}{Number of compounds.}
-
-\item{wd}{Directory under which results are archived.}
+\item{...}{Hand over to renderurl.}
 }
 \value{
-File path of the file table.
+Nothing useful.
 }
 \description{
-Generates file table.
+Render smiles from an online resource.
 }
 \author{
 Todor Kondić

man/presc.p.Rd → man/renderurl.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/mix.R
-\name{presc.p}
-\alias{presc.p}
-\title{Parallel version of presc.single}
+\name{renderurl}
+\alias{renderurl}
+\title{Render Compound from an Online Resource}
 \usage{
-presc.p(cl, fn_data, fn_cmpd_l, mode, ppm_lim_fine = 10,
-  EIC_limit = 0.001)
+renderurl(depictURL, coords = c(0, 0, 100, 100),
+  filename = tempfile(fileext = ".svg"))
 }
 \arguments{
-\item{cl}{Cluster object.}
+\item{depictURL}{The URL of the object to plot.}
 
-\item{fn_data}{Sequence of mzML files.}
+\item{coords}{The positioning of the image (in data coords).}
 
-\item{fn_cmpd_l}{Filename of the compound list.}
-
-\item{mode}{RMB mode.}
-
-\item{ppm_lim_fine}{See ReSOLUTION.}
-
-\item{EIC_limit}{See ReSOLUTION.}
+\item{filename}{Temp filename.}
 }
 \value{
 Nothing useful.
 }
 \description{
-Parallel version of presc.single.
+Helper function for rendersmiles2
 }
 \author{
 Todor Kondić