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ssayols / rrvgo

Reduce + Visualize Gene Ontology
GNU General Public License v3.0
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Is there a way of controlling what dots get labeled in the scatter plot? #15

Closed KTMD-plant closed 2 years ago

KTMD-plant commented 2 years ago

I am noticing that in many of my plots some dots do and some don't get labeled. I know the documentation says " the most representative term of the group"; but how does the most representative term get selected? Is there a way I could customize/control on this?

ssayols commented 2 years ago

Unfortunately scatterPlot() either labels the most representative term, or none. It is controlled with the addLabel parameter, which is by default set to TRUE.

The most representative term is, by definition, the term with the highest score within a group of terms that are "close". "Close" means that the distance that separates them as calculated by calculateSimMatrix() with the method of your choice, is below the similarity threshold you choose afterward in reduceSimMatrix(). This is explained in section 2.2 of RRVGO's vignette.

If you'd like to label other terms than the group's representatives, you should manipulate the ggplot2 object returned by scatterPlot().