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Logo

Generates 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

case3 properties motifs annot subset report

annotCols = id,class,family,medline,type,
selectCol = name


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