[PCA][PCA differential][PLS][PLS differential]
All the commands in this submenu start a 2D plot application and as many plotGrid applications as field blocks contains the dataset. The 2D plot and the grid plots are intrinsically interconnected in such a way that the interaction of the User on the 2D plot will be immediately shown in all the grid plots.
The 2D application and the plotGrid application, when working together in an active plot, have essentially the same functionality than their stand-alone version, so please refer to the links in the previous paragraph for further reference regarding commands, options, etc...
Notice that this is a "tear-off menu", if you click on the dotted line on top of the menu you will transform the submenu in an independent window which will remain open until you specifically close it. This allows a fast access to the plots and is particularly useful when you plan to open many plots at the same time.
This command opens:
The User can click with the mouse in any point of the scores plot. A red cross is represented to mark the point. GOLPE extracts the values of the scores for this point (t1 and t2) and projects back these values into the original space using the PCA scores (P) to generate "pseudo-fields" which are represented in the grid plots.
The meaning of the pseudo-fields is equivalent to the meaning of the original fields used to obtain the PCA; energies of interaction between the ligands and probes. The difference is that is obtained by a back-projection form a simplified model and therefore only the part of the variance explained by the two first PC's of the PCA model is represented. Also, it is possible to obtain pseudo-fields for "theoretical compounds", not actually representing an object in the series.
For example: if the series contains two separate clusters of objects if is possible to click somewhere in between them to see how it would be like a compound sharing characteristics of the two clusters. Clicking in the middle of each clusters would produce a representation of the main characteristics which identify each cluster in the model, corresponding to the part of the variance explained by the two first PC's.
Plot>>>active plots>>>PCA differential
This command opens:
The User should click twice on the scores plot. A red arrow is drawn between the first and the second clicked point (A and B points). GOLPE extracts the differences in the values of the scores for this point (tB1-tA1 and tB2-tA2) and projects back these values into the original space using the PCA scores (P) to generate differences in "pseudo-fields" which are represented in the grid plots.
The meaning of these differences in pseudo-fields is equivalent to the meaning of differences of original fields computed for any two objects, as those that can be obtained using the command plot>>>Grid plots>>Objects differences. The difference is that is obtained by a back-projection form a simplified model and therefore only the part of the variance explained by the two first PC's of the PCA model is represented. Also, it is possible to obtain differences in pseudo-fields for "theoretical compounds", not actually representing an couple of object in the series.
For example: if the series contains two separate clusters of objects if is possible to click in the middle of each clusters, to obtain a representation of the main characteristics which differentiate both clusters, corresponding to the part of the variance explained by the two first PC's. Drawing an arrow from a real compound or cluster of compounds to an empty region in the scores plot would represent the changes in the field required for the initial compounds to reach this region. A rational use of this plot can be very useful for the design of new compounds.
This command opens:
The User can click with the mouse in any point of the PLS scores plot. Please notice that, since the PLS scores plot are extracted to correlate with the Y, the points at the right top corner represent the most "active" compounds, while those at the left bottom corner represent the less active ones. A red cross is represented to mark the point. GOLPE extracts the values of the PLS scores for this point (t1 and t2) and projects back these values into the original space using the PCA scores (P) to generate "pseudo-fields" which are then multiplied by the values of the PLS pseudo coefficients (for a model of two components). The values obtained, the pseudo-activity contributions, indicate the contribution to increase or decrease the activity of the field values around this particular pseudo-object.
The meaning of this pseudo-activity contribution fields is equivalent to the meaning of the original Activity Contribution plots obtained with Plot>>>Grid plot >>Activity Contributions. The difference is that is obtained by a back-projection form a simplified model and therefore only the part of the variance explained by the two first LV's of the PLS model is represented. Also, it is possible to obtain pseudo-activity contributions for "theoretical compounds", not actually representing an object in the series.
For example: if the series contains two separate clusters, clicking in the middle of each clusters would produce a representation of the main field interactions which increase or decrease the activity for each cluster in the model, corresponding to the part of the variance explained by the two first PC's.
It is also possible to click on regions of the PLS scores plot which are empty, showing which would be the field value contributions to the activity of theoretical points placed in this position. Two specially interesting regions are the top right and the left bottom corners of the plot, the information gathered here would show the features that the model consider necessary for obtaining the most and the less active compounds respectively.
Plot>>>active plots>>>PLS differential
This command opens:
The User should click twice on the scores plot. A red arrow is drawn between the first and the second clicked point (A and B points). GOLPE extracts the differences in the values of the PLS scores for this point (tB1-tA1 and tB2-tA2) and projects back these values into the original space using the PCA scores (P) to generate differences in "pseudo-fields". These are not shown, but multiplied by the values of the PLS pseudo coefficients (for a model of two components). The final values obtained, the differences in pseudo-activity contributions, indicate the differences in the field contributions that increase or decrease the activity for the two pseudo-objects represented by the clicks.
The differences in pseudo-activity contribution fields in between two real or hypothetical objects A and B represent the reasons, from the model point of view, explaining the differences in activity of these two objects. These are shown in terms of the contribution of each grid position, and therefore highlights the regions which contribute most to explain why A is more active than B or viceversa. In this contexts, the activity contributions have the same meaning that the values obtained with Plot>>>Grid plot >>Activity Contributions. The difference is that is obtained by a back-projection form a simplified model and therefore only the part of the variance explained by the two first LV's of the PLS model is represented. Also, it is possible to obtain pseudo-activity contributions for "theoretical compounds", not actually representing an object in the series.
It is also possible to click an arrow starting or pointing to regions of the PLS scores plot which are empty, showing which would be the changes in the field value contributions to the activity of theoretical points placed in this position. Two specially interesting regions are the top right and the left bottom corners of the plot, the information gathered here would show the features that the model consider necessary for obtaining the most and the less active compounds respectively. A rational use of this plot can be very useful for the design of new compounds.