The Shinyscreen Package

Usage

Prescreening with presc.plot

1. Generate prescreening data frames,

   presc.do(list.files(path="~/ECI_SCRATCH/20190627_HEROBER",patt=".*.mzML",full.names=T),
            mode="pH",fn_cmpd_l="./cutlist.csv",proc=F,dest=".")
       

   This is to be carried out inside the directory containing the mzML files. For sequential execution, leave out the proc argument.

2. Plot,

   require(shinyscreen)
   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")
       

   The only argument is a sequence of absolute paths to directories containing the prescreen data. The resulting plot file is going to be placed into the current working directory.

Prescreening with presc.shiny

1. Same as above
2. To start the Shiny prescreening, do

   require(shinyscreen)
   df<- data.frame(Files=rep("file.mzML",15),ID=1:15,tag=rep(c(15,30,45),5),set_name="Collision Energy")
   This dataframe is the input that has to be introduced in order
   to have all the information from the data.
   
   pos_wds <- list.files(".",patt=".*2019.*_[49][35]$",include.dirs=T,full.names=T)
   This is an example of using the POS data (pH). 
   
   presc.shiny(pos_wds,mode="pH",cex=1,prescdf=df)
   The arguments which need to be put into the presc.shiny are
   pos_wds (as an example), the mode (pH or mH), cex as a font size
   and prescdf=df to get the information into the shiny part.