Thanks for using q2-SCNIC. Are you visualizing the
network.gml file that comes from running
make-modules-on-correlations or from
build-correlation-network-r? The network that results from
make-modules-on-correlations does not include negative edges because it is showing the network that was used to generate modules. Module making does not include negative edges because you do not want negatively correlated features in the same modules as it would mess up summarization of the features in them.
If you want to see your network without modules then you can export the
network.gml from the
.qza which you create from
build-correlation-network-p. This will not show you your modules though. If you want to see negative correlations and modules then you can use cytoscape to export the module data from the
make-modules-on-correlations and then add it to the
Alternatively you could use the summarized feature table
make-modules-on-correlations to run
calculate-correlations. Then run
build-correlation-network-p with that correlation
.qza to get a correlation network where modules are represented as a single node. This would show you negative correlations but not all the underlying correlations between the features with make up a module.