Up: Component summary Component

ExperimentSetup

Creates a report that displays all sample groups using a table and a graph that visualizes the sample groups and their relations. Also, ID sets (if provided) are summarized in a table and also into the graph. Example graph

Version 1.2
Bundle microarray
Categories Latex
Authors Kristian Ovaska (kristian.ovaska@helsinki.fi)
Issue tracker View/Report issues
Requires R ; igraph (R-package)
Source files component.xml ExperimentSetup.r
Usage Example with default values

Inputs

Name Type Mandatory Description
groups SampleGroupTable Mandatory Sample groups.
idlist SetList Optional ID sets for groups defined in 'groups'. If this input is given, the names and sizes of ID sets are shown in the graph. The sets must contain the annotation SampleGroup that binds each set to a sample group.

Outputs

Name Type Description
report Latex Experiment setup report that includes a table that contains all sample groups and a graph that visualizes their relations. Also contains a table that summarizes all ID lists provided.
graph GraphML A graph that visualizes the experiment setup. The graph can be rendered using GraphVisualizer. If the number of samples is low, a hierarchical layout may work. Otherwise, try a spring layout with overlap=false.

Parameters

Name Type Default Description
definWidth float 8 Width of the definition column (cm)
descWidth float 7 Width of the description column (cm)
sectionTitle string "Experiment Setup" Title for a new latex section. If non is given, a new section is not created.
sectionType string "section" Type of LaTeX section: usually one of section, subsection or subsubsection. No section statement is written if sectionTitle is empty.

Test cases

Test case Parameters IN
groups
IN
idlist
OUT
report
OUT
graph
case1 (missing) groups (missing) report graph
case2 (missing) groups idlist report graph

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