isobar-reports {isobar} | R Documentation

## Isobar reports

### 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

[Package isobar version 1.28.1 Index]