isobar-reports: Isobar reports

In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description

Generation of LaTeX and XLS reports is helped with functions which facilitate the gathering of relevant information and creation of tikz plots. create.reports parses properties (by calling load.properties) and initialize environments and computations (by calling initialize.env) required by the reports, calls Sweave and pdflatex.

Usage

create.reports(properties.file = "properties.R", 
               global.properties.file = system.file("report","properties.R", package = "isobar"),
               args = NULL, ...,
               recreate.properties.env = TRUE, recreate.report.env = TRUE)

load.properties(properties.file = "properties.R",
                global.properties.file = system.file("report","properties.R",package="isobar"),
                args = NULL, ...)

initialize.env(env, properties.env)

Arguments

properties.file	File which holds the parameters for data analysis and report generation. It is parsed as R code after the global report configuration file global.properties.file and defines peaklists, identification files, significance levels, etc. See the global properties file for the available options and values.
global.properties.file	system.file("report","properties.R",package="isobar")
args	Additional (command line) arguments which overrids those in properties.file.
...	Additional properties.
recreate.properties.env	Whether a properties.env existing in the global environment should be used, or it should be recreated.
recreate.report.env	Whether a report.env existing in the global environment should be used, or it should be recreated.
env	Item to be initialized.
properties.env	Environment into which properties are read.

Details

The directory inst in the isobar installation directory system.file("inst",package="isobar") contains R, Sweave, and LaTeX files as examples of how to create XLS and PDF reports using isobar.

create_reports.R

Call with Rscript. It is the main file which

1. parses command line options. --compile and --zip are parsed directly and given as arguments to create.reports. Other arguments are given load.properties.

2. calls a perl script to generate a XLS report

3. generates a LaTeX quality control and analysis report

for the XLS report the script pl/tab2xls.pl is used, which concetenates CSV files to a XLS. See Perl requirements. Sweave is called on report/isobar-qc.Rnw and report/isobar-analysis.Rnw. All files are written the working directory.

isobar-qc.Rnw

Quality control Sweave file.

isobar-analysis.Rnw

Data analysis Sweave file.

properties.R

Default configuration for data analysis.

report-utils.tex

LaTeX functions for plotting tikz graphics, etc.

Author(s)

Florian P Breitwieser

See Also

IBSpectra, isobar-preprocessing isobar-analysis

isobar documentation built on Nov. 8, 2020, 7:48 p.m.