The BnPredict plugin displays nodes in colors that contain a great deal of significance. The display may use either a two-color system (default) or a multi-color system. Many find the two-color system to be more understandable and logical, though it discards potentially important information. The multi-color system is more complex as incorporated an additional color-dimension. The two-color system is simpler and may be more visually intuitive to the user. Bin probabilities of over expression and under expression are compared while the neutrally expressed bin is ignored.
If the over expressed bin is more probable than the under expressed bin, the node will appear as a shade of the up-color. The relative dominance of expression (either under or over) will determine the intensity of the expression color. Equal probabilities for the up bin and down bin will result in a white node. The following example might explain the 2-color system.
In this example (subset of the network shown), we can see that
the network has been perturbed at gene CCL5 where it has been set to under expressed. A quick visual examination shows that the result of a down regulation of gene CCL5 has an immediate impact on its direct children. Both genes BAD and UBE2L3 can be seen to be significantly more likely to be under expressed when CCL5 is in the down state. As we move downstream in the network we can see that the effect on gene WARS is also towards down-regulation, but the faintness of the color would indicate that there is a significantly reduced response. On the other arm, we see that the grandchild node, ESRRA has a greater relative probability of being over expressed. This might suggest that there is an inhibitory relationship between ESRRA and UBE2L3. The white color of gene NUCB1 indicates that responses have significantly diminished that far down the network. No other genes have been affected by this perturbation in this network. The multi-color system uses a similar approach as the two-color system, but includes the information contained in the neutral bin. The neutral bin's probability affects the color brightness. A more probable bin will result in a darker color. For example, a node which is frequently over-expressed, rarely neutral and rarely under-expressed will appear brighter than a node which is frequently over-expressed, frequently neutral and rarely under-expressed. In this example, the two-color system would treat the two nodes as equal while the multi-color system makes a distinction.
The specific probabilities that the coloring system uses depends on the currently selected display selection. When Probability is selected in the BnAttribute Panel, the coloring scheme will use the raw bin probability tables. When the Probability Change button is selected, each node's bin probability will be compared to the original bin probability. In this case relative changes in bin probability as a result of network perturbations are more easily observed visually.
By clicking the Up-Color or Down-Color buttons, users may select a desirable color scheme. For both coloring systems, the color sensitivity bar allows the user to adjust BnPredict's color sensitivity so that changes can be visually discernible relative to others in the network.