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Commit c3aac674 authored by Todor Kondic's avatar Todor Kondic
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Updated: README.org

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README.org
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Provided Shinyscreen is successfully installed this snippet will
run it.
#+BEGIN_SRC R
library(shinyscreen)
PROJECT="project/location/somewhere/on/my/storage/device"
launch(projDir=PROJECT)
shinyscreen::app()
#+END_SRC
The `projDir` argument can be left out in which case shinyscreen is
going to assume that the project directory is the result of
#+BEGIN_SRC R
## Get current working directory of R instance.
getwd()
#+END_SRC
So, what is the /project directory/? This is the place where
shinyscreen state, log and output files go by default. In other
words, if you produce some PDF plots, this is where they are going
to end up.
* Usage
** Before Starting
*** Compound Lists
The lists of known and unknown compounds contain different
information and are treated differently. The application needs at
least one, but can take both known and unknown lists as
inputs. The formats of both lists are explained below.
**** Known Compounds List
- A comma-separated CSV file table.
- The column names are case-sensitive.
- Required headers:
- ID :: This is an integer compound identifier. This column
must be filled and each ID entry must be unique. If
both unknown and known lists are given, IDs from both
lists must not overlap.
- SMILES :: The /SMILES/ character string. Shinyscreen accepts
only MS-Ready SMILES. This column must be filled.
- Name :: The compound name. This column can be left empty.
- RT :: The retention time of the peak in minutes. This column
can be left empty.
- Optional headers:
- mz :: m/z mass of the compound. If both SMILES and mz entries
are present for a given compound, mz takes precedence.
#+CAPTION: The first few rows of a compound list containing known compounds.
#+BEGIN_EXAMPLE
"ID","Name","SMILES","RT"
33,"Isoproturon","CC(C)C1=CC=C(NC(=O)N(C)C)C=C1",19.6
717,"epsilon-Decalactone","CCCCC1CCCCC(=O)O1",
67,,"CCCCC1CCCCCC(=O)O1",
...,...,...,...
#+END_EXAMPLE
It is *strongly suggested* to quote all the character strings, such
as SMILES and Name.
**** Unknown Compounds List
- A comma-separated CSV file table.
- Required headers:
- ID :: This is an integer compound identifier. This column
must be filled and each ID entry must be unique. If
both unknown and known lists are given, IDs from both
lists must not overlap.
- mz :: m/z mass of the compound.
- RT :: The retention time of the peak in minutes. This column
can be left empty.
#+CAPTION: The first few rows of a compound list containing unknown compounds.
#+BEGIN_EXAMPLE
"ID","mz","RT"
22,296.1160,
888,503.2816,
#+END_EXAMPLE
*** The compound sets.
Shinyscreen organises its data around the concept of compound
sets. If, given a collection of data files, it is possible
to break down the compounds into logical groups, shinyscreen
will make it easier to navigate different groups if this is
specified in a CSV list. In this case, the CSV file contains two
columns: *ID* and *set*. The *ID* is the identifier of the
compound from the compound list and *set* is a name of the
set. If there is no sensible way of splitting compounds in
groups, it is enough to copy all the ID-s from the compound list
into a new CSV and use any character string to fill out the
*set* column.
#+CAPTION: The first few rows of a compound set.
| ID | set | RT |
|-----+------+----|
| 33 | mixA | |
| 717 | mixA | |
| 999 | mixA | |
| ... | ... | |
| 129 | mixB | |
| 516 | mixB | |
| ... | ... | |
| 333 | mixC | |
| 999 | mixC | |
*** Data files
These should be in mzML format.
** Sets, Tags, Adducts, Files and IDs
Each file is labelled by a tag, adduct and set. Sets are defined in
the compound set CSV file and group compounds according to their
IDs. Adducts correspond to the adducts. Tags label files in the
plots.
For known compounds, each set can contain multiple adducts. Sets of
unknowns can only contain a single adduct. Any files belonging to the
same set that have been acquired in a single adduct, must carry
unique tags.
In addition, the IDs of compounds belonging to the same set/adduct
combination must be unique. Different ID sets may overlap.
Essentially, sets serve the purpouse of visually grouping files in
the plots. Also, set combines those groups of files with particular
collections of compounds (from the compound set CSV file).
** Config Screen
This is the start tab. Import the compound and set lists first,
then proceed to import the mzML files. Provide tags in the tag text
box and then assign the sets, adducts and tags to the imported mzML
files using table widget. Once this is done, move on to the
~Spectra Extraction~ tab.
*** Resetting State
In case some inputs have been changed, but the program for some
reason does not seem to respond to those changes, perhaps
resetting the state using the button ~Reset State~ will help. This
will clean the current compound state tables (but, all the inputs
remain unchanged).
*** Switching Projects
The ~Switch project.~ button can be used to start new projects, or
change between them in the middle of processing.
Switching projects while the program is running makes most sense
if it is desired to change some of the inputs (e.g. different set
configuration, or same compound lists but different files) while
retaining the others. The user is presented with a directory
change dialogue which is then used to select the new project
directory. If needed, a new project directory can be created from
the same dialogue. All the inputs that currently exist on the
configuration tab will be kept during switching. This way, only
what needs to be changed can be changed.
** Spectra Extraction
Set the extraction parameters and then select a certain number of
sets to scan for. This may take a while.
After one, or more sets have been extracted (once the status box
gets checked), it is possible to carry out the auto quality
check. This check is going to perform a rudimentary analysis of the
spectra, as well as retrieve the retention times of the precursor
peaks and their MS2 spectra. This procedure must be done in order
to plot the MS2 spectra.
TODO: Explain the parameters
For entries that had RT empty, the entire retention time interval
is scanned for peaks. Those entries with known RT will only be
scanned within the interval specified by the parameters (by default
1 min). This means that the processing is going to take much less
time then for the case if RT was left out.
** Prescreening
The third tab allows the visual inspection of the spectra and the
chromatogram, as well as exporting the plots in a PDF format.
* Usage
Shinyscreen (version > 1.0.0) is a self-documented application. The
best way to learn about using Shinyscreen is by running it. Please
let us know if we can improve on that documentation.
* Thanks
Many thanks to the students of the *Masters in Integrated Systems Biology*
......
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