element;intro
#Welcome;Welcome to the interactive tour for <code>GeneTonic</code>!<br><br>Here you will get to know the functionality included in the <b>Gene-Geneset Graph panel</b>.
#mymenu;Here is where you can move around the different tabs of <code>GeneTonic</code>.
#shiny-tab-tab_ggs;This is the main content of the Gene-Geneset Graph tab. This tab mainly displays a bipartite graph of genes and genesets, with the aim of making the exploration of their relationships easier, and allowing also the in-depth exploration of the single network nodes.
#ggsnetwork;This is where the main network will be displayed. The number of nodes displayed depends mainly on the number of gene sets that you will decide to include.
#controlbar-toggle;You can control this by clicking on the controlbar toggle...
#n_genesets;... and changing the number of genesets.
#controlbar-toggle;Close back the controlbar.
#ggsnetwork;You can interact with the network visualization, either by clicking on a desired node (you can zoom in with the mouse wheel of with the trackpad)...
#nodeSelectggsnetwork;... or by selecting one here - first the gene sets are displayed, then the genes. Now select a gene set of interest.
#ui_ggs_genesetbox;Whenever you select something, some additional content gets displayed in the boxes on the right side. If you selected a gene set, you should see some summary information on the geneset, referred to the inputs you provided, below a signature heatmap and a signature volcano plot including all the genes annotated to the gene set.
#ggsnetwork;You can go back to the main network view, and select a gene now.
#ui_ggs_genebox;See how some links to the selected gene get automatically generated as action buttons - to the NCBI and the GeneCards databases.
#controlbar-toggle;Toggle again the control bar...
#exp_condition + .selectize-control;... and select for example 'condition' from the dropdown select input...
#col; ... or you use the <b> Select color for volcano plot </b> option. With this you can change the color and transparency and the genes of the chosen geneset will be displayed accordingly.
#labels; Also you can decide to check the <b> Display all labels </b> box. This will add the names of all genes in the geneset to the signature volcano plot - otherwise only a small number is displayed to keep a clearly represented plot. 
#controlbar-toggle;Close back the control bar.
#ui_ggs_genebox;You can see how the gene infobox also added a plot on the selected gene, split by the factor you specified in the select widget.
#ggsnetwork;You can be interested in a number of genes and gene sets. <code>GeneTonic</code> supports functions for bookmarking all these entities and combine them together in an HTML report. Select any node now...
#bookmarker;... and click on the Bookmark button in the navbar. You can repeat this action as many times as desired.
#ggsnetwork;To simplify the action of bookmarking many entities which might be close to each other, the bookmarking can be triggered also by pressing the <code>left Ctrl</code> key on your keyboard. Try doing so, and keep track of the app notifying you the node has been added to the lists of genes and genesets of interest.
#shiny-tab-tab_ggs;You can edit the number of displayed genesets to change the granularity and detail level of the graph, and again bookmark nodes of interest.
#ui_graph_summary; This table lists the individual genes and their respective degree. In this connection, the degree of a gene is the number of connections of this genes in the above graph. Besides the gene name and the degree, the table also provides more information on the genes. The buttons of the 'See more' column link you directly to the NCBI, Genecards and GTEx databases, where more information of the respective gene is available. 
#thanks;Thank you for taking the Gene-Geneset panel tour of <code>GeneTonic</code>!
