Up: Component summary
Up: Component summary
Component
ClusterReportPerforms a hierarchical clustering of samples. The clustering is based on the given numeric row values of the numeric matrix and the results are shown on a LaTeX report fragment.
| Version | 1.1 |
|---|---|
| Bundle | tools |
| Categories | Latex Clustering |
| Authors | Kristian Ovaska (kristian.ovaska@helsinki.fi), Marko Laakso (Marko.Laakso@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | R ; cluster (R-package) ; igraph (R-package) |
| Source files | component.xml ClusterReport.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| matr | Matrix | Mandatory | Numeric data |
Outputs| Name | Type | Description |
|---|---|---|
| report | Latex | Clustering report |
| tree | GraphML | Cluster dendrogram |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| cexSampleText | float | 1.0 | A numerical value giving the amount by which the sample names in the plot tree should be scaled relative to the default values. |
| clusterMethod | string | "average" | Name of clustering method. One of 'average', 'single' or 'complete'. |
| margin | float | 0 | A numerical value giving the amount by which margin is increased. |
| rotateLabels | boolean | true | If true, rotate column labels vertically in the distance matrix so that they take less space on the x axis. |
| sectionTitle | string | "Sample clusters" | Title of the LaTeX section |
| sectionType | string | "subsection" | Type of LaTeX section: usually one of section, subsection or subsubsection. If empty, no section statement is written. |
| showDistance | boolean | true | This flag tells if the distance matrix shall be included into the document |
| width | float | 16 | Width of diagram in cm |
Test cases| Test case | Parameters▼ | IN matr |
OUT report |
OUT tree |
||
|---|---|---|---|---|---|---|
| case1 | (missing) | matr | report | tree | ||
| case2_twocolumns | properties | matr | report | tree | ||
|
showDistance = false, |
||||||
| case3_empty_input | (missing) | matr | report | tree | ||