not clear from the manual that all genes in the heatmap will be used for the search
(for example, it could have been only the leading edge genes)
enhancement : would it be possible to select a few genes or all genes using mouse selection
was intuitively trying to get the interface by right clicking on a node: would it be more intuitive than the heat map menu bar or would it create issue with other apps?
Idea: Have a single menu option (in both Heat Map and right-click menus) that says something like "Show In...". This opens a dialog that displays the list of genes with checkboxes. The individual genes can be selected or not, and there's buttons for "select all", "select none", "select leading edge". Theres also a combo box to select the app to use (genemania or string etc).
This would give the user fine grained control over exactly which genes to select (eg if they just want the leading edge). And I think it would make it more clear as to what's going on. For example if you right-click a node and select "Show in GeneMANIA" and then a new network appears, is it clear that the genes from the node where selected for the new network? Showing the list of exactly which genes are being used before creating the network would be more clear I think.
Idea: Have a single menu option (in both Heat Map and right-click menus) that says something like "Show In...". This opens a dialog that displays the list of genes with checkboxes. The individual genes can be selected or not, and there's buttons for "select all", "select none", "select leading edge". Theres also a combo box to select the app to use (genemania or string etc).
This would give the user fine grained control over exactly which genes to select (eg if they just want the leading edge). And I think it would make it more clear as to what's going on. For example if you right-click a node and select "Show in GeneMANIA" and then a new network appears, is it clear that the genes from the node where selected for the new network? Showing the list of exactly which genes are being used before creating the network would be more clear I think.