Shapes

The "Shapes" graph draws regions as various geometric shapes depending on the region type. This graph type is primarily designed to be used with motif tracks, where it allows repeating patterns of motifs (i.e. potential cis-regulatory modules) to better stand out since the different TFBS regions will be discernable by both color and shape. It is also a visually aesthetic graph type that is suitable for presentations or for creating figures for publications. Once this plugin is installed, you can change to this graph type by right-clicking on a region track in the Features Panel and selecting "Shapes" from the "Graph type" menu.

Graph settings

The appearance of the track can be configured by right-clicking on a region track with this graph type in the Features Panel and going to "Graph Settings" in the context-menu.

Shapes

Default shapes are assigned based on the Transfac classification of the different motifs, as shown in the table below. Motifs that do not have a classification property will default to the "Rounded Square" shape, whereas all regions that are not motifs will default to "Square". It is possible to override the default shapes and choose your own preferences by selecting "Shapes..." from the "Graph Settings" context-menu. This will bring up a dialog with a table listing all currently assigned shapes. By selecting one or more rows from this table and right-clicking, you can choose a new shape from a context-menu. Once a shape has been selected for a region type, it will apply to all tracks (similar to how region colors also apply to the same region types across all tracks).

Basic domain TFs are different quadrilaterals (except Diamond). Zinc-fingers have concave shapes (except Star). Helix-Turn-Helix are other regular concave shapes (plus Star). Beta-scaffold factors with minor groove contacts have curved shapes (plus Chest). Other motifs (including motifs without classifications) default to rounded square.

TF class	Transfac Classification	Shape
Basic Leucine zipper (bZIP)	1.1	Square
Basic Helix-loop-helix (bHLH)	1.2	Parallelogram
bHLH-ZIP	1.3	Trapezoid
Basic Helix-span-helix	1.6	Trapezoid Down
Other basic domains	1.x	Square
Nuclear Receptors (Cys4 zinc fingers)	2.1	Cross
Other Cys4 zinc fingers	2.2	Cross
Cys2His2 zinc fingers	2.3	Castle
Cys6 zinc fingers	2.4	Diabolo
Other zinc fingers	2.x	Hourglass
Homeo domain (only)	3.1.1	Triangle
Homeo domain plus other domain	3.1	Triangle Down
Paired domain	3.2	Diamond
Forkhead	3.3	Pentagon
Heat shock factor	3.4	Star
Tryptophan clusters	3.5	Hexagon
Other Helix-turn-helix	3.x	Octagon
RHR	4.1	Chest
STAT	4.2	Half Moon
MADS	4.4	Quatrefoil
High Mobility Group	4.7	Half Moon Down
Other beta-scaffolds	4.x	Circle
Other TFs	0.x	Rounded Square

Bevel effect

If the "bevel effect" option is selected, the region shapes will be drawn as slightly three-dimensional figures with shades and lighting. If the option is disabled, the shapes will just be drawn with "flat" colors.

Shape Width

Normally, a region shape is drawn so that its width spans the actual length of the region (i.e. the drawing is "to scale"). In this case, a region that is 6 bp wide will be drawn so that it covers 6 bp, and it will appear half as wide as a 12 bp region. However, this graph type also supports drawing the shapes with fixed sizes. When this option is selected, the width of the shape will depend neither on the region width nor the zoom-level. The width can be either small (30 pixels), medium (60 pixels) or large (100 pixels).

Draw DNA Helix

This option will draw a DNA double helix behind the regions. This is purely "eye candy" to enhance the appearance of the visualization. The helix will be aligned vertically in the middle of the track, and the size of the helix can be scaled according to the height of the track, either small (20% of height), medium (30%), large (50%) or very large (70%). If one of these relative sizes are selected, the helix will shrink or grow if the height of the track is changed. It is also possible to select "True scale". In this case, the helix will always be drawn with a period of 10.4 bp, so adjusting the zoom-level will cause the helix to change in size (but changing the height of the track will not affect the size of the helix). In expanded mode, each row of regions will be drawn with their own double helix (which can be a bit confusing, since it would then appear as if the regions are located on different strands of DNA).

Top and bottom margins

It is possible to add a top- and/or bottom-margin to the track to create some vertical space between the shapes and the top and bottom edges. The size of the margins can be either absolute (specific size in pixels) or relative to the height of the track (in percent). Margins are a good way to adjust the vertical position of the shapes when labels are drawn.

Type labels and orientation indicators

If you select "Draw Type Labels" from the "Graph Settings" menu, the type of the region will be displayed beneath the region shape. Note that the colors used for the labels are usually "dynamic", meaning that it will be BLACK if the color of the region is bright and WHITE if the color of the region is dark. This is the same strategy that is used in the default graph type, where the labels are drawn on top of the region. However, since the labels are here drawn beneath the region, they could disappear into the background if the background color is WHITE (or BLACK). To explicitly set the label color, select "Label Color" from the "Graph Settings" context-menu.

If type labels are shown and the "Indicate orientation" option is selected, the orientation of a region (relative to the currently visualized orientation of the sequence!) will be indicated with green or red arrows next to the type labels.