GLAD allows you to view the structures of the glycans (and glycopeptides) for the data on the fly provided the Name of the glycans (or glycopeptides) are in the CFG format. You can view the glycans at any time by pulling out the “Glycan Structure” drawer and placing your mouse over a data point, i.e.:
- a bar in a bar graph
- a tile in a hetmap
- a node in a force graph
- a point in the scatter plot
- a bubble in the bubble box plot
Clicking on the in the top right of the structure can save the svg image file of the structure.
The “Glycan Structure” drawer also contains the settings used to draw the glycans.
- Delay Time for Drawing: This is how many milliseconds the application will wait before drawing the structure. You can increase this number if you would like it to “stick” to one structure and not change often. Increasing this will also reduce the performance it requires.
- Symbol Size: Controls the size of the monosaccharide symbols.
- Drawing type:
- Fixed Glycan Scaling- In this method, the glycans are scaled by their size and hence shorter glycans will appear shorter as compared to longer glycans.
- Fit Glycan in Box- In this method, the glycans are drawn in a box with fixed dimensions regardless of how long or short the glycan is.
- Fucose Drawing Options (v2 onwards):
- Fucose Outwards – Is the default and draws the fucoses at the same level as its parent monosaccharide and puts them outward from the center on either side of branches.
- Fucose Left – This option puts the fucose on the left of the branch regardless of if the branch is on the left or right of the center.
- Fucose Name Dependant – This option puts the fucose on either left or right of the branch depending on how it occurs in the name.
- Fucose GLAD 1.0 – This option uses the classical v1.0 method of drawing fucoses.
To view multiple structures for data which you may find interesting, you can Ctrl+Click on the data points to put the structures in the “Selected Structure” popup. Clicking on the Selected Structure button will open up the popup with all the structures drawn inside it.
Each glycan/glycopeptide structure also appears with a next to it to save the svg image of that structure. A list of suggested classes also appears below the structure (note- this is still not fully tested and can give errors for some types of glycans so please use this classification with caution).
You can clear the structures by clicking on the “Clear All Structures” button in the popup.