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Up: Component summary
Component
ExperimentSetupCreates 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 |