Up: Component summary
Up: Component summary
Component
LogoGenerates sequence logos for the given DNA motifs. You may link to these figures using a syntax of \hyperlink{logo.INSTANCE-MOTIF}{TEXT}, where INSTANCE is the name of the Logo component instance, MOTIF is the name of the motif and TEXT represents the actual link label.
| Version | 1.6 |
|---|---|
| Bundle | microarray |
| Categories | Sequence Motif Latex |
| Authors | Marko Laakso (Marko.Laakso@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | R ; seqLogo (R-bioconductor) |
| Source files | component.xml Logo.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| motifs | MotifSet | Mandatory | Input motifs. |
| annot | AnnotationTable | Optional | Additional information about the markers. |
| subset | CSV | Optional | Select only those motifs that are present in one of the columns. See parameter selectCol. |
Outputs| Name | Type | Description |
|---|---|---|
| report | Latex | Latex fragment containing the visualizations. LaTeX-label for the figure is fig:instanceName, where instanceName refers to the name of the pipeline component used in the network configuration. Individual motifs are drawn in subfigures. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| annotCols | string | "" | Comma separated list of annotation columns if not all are to be shown. |
| caption | string | "Consensus sequences of the motifs." | Caption of the figure. |
| figN | int | 12 | Number of motifs per one LaTeX figure. |
| selectCol | string | "" | A column of subset. Motifs that are present in this column are selected from motifs. The first column is used if this value is empty. |
Test cases| Test case | Parameters▼ | IN motifs |
IN annot |
IN subset |
OUT report |
|
|---|---|---|---|---|---|---|
| case1 | (missing) | motifs | annot | (missing) | report | |
| case2 | properties | motifs | annot | (missing) | report | |
|
annotCols = sites |
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| case3 | properties | motifs | annot | subset | report | |
|
annotCols = id,class,family,medline,type, |
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