HTML MotifTable

Description

The HTML_MotifTable format will output an HTML-formatted table with one motif on each row and with columns containing information about different motif properties chosen by the user. It is possible to include graphical sequence logos for the motifs and also specify alternative motif properties to be shown as tooltips when the user points at a cell in the table.

Arguments

Name	Description
Format	This parameter specifies which motif properties to include in the output as an ordered, comma-separated list of property names. Note that standard properties are case-insensitive, but user-defined properties are case-sensitive! Standard motif properties include: ID Short name Long name Consensus Size IC-content GC-content Factors Classification Class name Classpath Quality Part Alternatives Interactions Organisms Expression Matrix Logo The name of a property can be followed by the name of another property within parenthesis. This second property will be displayed as a tooltip when the mouse is over the table cell with the first property. For example, the format string: "`ID,Short Name(Long Name)`" will create a table with two columns where the first column will contain the motif ID and the second the motif's short name. If the user points the mouse at the short name of a motif, its long name will be displayed in a tooltip. (Note that this might not work within MotifLab but should work if the HTML document is saved to a file and displayed in an external web browser).
Sequence logo height	The height of the sequence logos (if logos are included).
Sequence logo width	The maximum width of sequence logos. If this is specified, logos will be scaled to fit within this limit when necessary. A value of 0 means no limit.
Sequence logos	Specifies whether the image files for motif sequence logos should be made specifically for this output data object and given file names reflecting this fact ("New images") or if the image files should be named after the motifs themselves (e.g. "M00134.gif") and allowed to be shared by other HTML-formatted output data objects that also contain sequence logos for the same motifs ("Shared images").
multiline	Some motif properties may be represented by lists (e.g. binding factors and alternative motif models). If the "multiline" option is selected, these lists will be broken across multiple lines in a table cell. If the "multiline" option is not selected, these properties will be output as comma-separated lists.
Headline	An optional headline which will be displayed above the table.

Name

Description

Format

This parameter specifies which motif properties to include in the output as an ordered, comma-separated list of property names. Note that standard properties are case-insensitive, but user-defined properties are case-sensitive!

Standard motif properties include:

ID
Short name
Long name
Consensus
Size
IC-content
GC-content
Factors
Classification
Class name
Classpath
Quality
Part
Alternatives
Interactions
Organisms
Expression
Matrix
Logo

The name of a property can be followed by the name of another property within parenthesis. This second property will be displayed as a tooltip when the mouse is over the table cell with the first property. For example, the format string: "ID,Short Name(Long Name)" will create a table with two columns where the first column will contain the motif ID and the second the motif's short name. If the user points the mouse at the short name of a motif, its long name will be displayed in a tooltip. (Note that this might not work within MotifLab but should work if the HTML document is saved to a file and displayed in an external web browser).

Sequence logo height

The height of the sequence logos (if logos are included).

Sequence logo width

The maximum width of sequence logos. If this is specified, logos will be scaled to fit within this limit when necessary. A value of 0 means no limit.

Sequence logos

Specifies whether the image files for motif sequence logos should be made specifically for this output data object and given file names reflecting this fact ("New images") or if the image files should be named after the motifs themselves (e.g. "M00134.gif") and allowed to be shared by other HTML-formatted output data objects that also contain sequence logos for the same motifs ("Shared images").

multiline

Some motif properties may be represented by lists (e.g. binding factors and alternative motif models). If the "multiline" option is selected, these lists will be broken across multiple lines in a table cell. If the "multiline" option is not selected, these properties will be output as comma-separated lists.

Headline

An optional headline which will be displayed above the table.

output

Motif_Properties