This navigation bar is open by default, however some options are not available immediately after loading the page (don't worry, proper errors will raise if something goes wrong). Here is the general aspect of the Top navigation bar:
Button that opens the side menu.
Button that resets colors of all plasmids/nodes and clears every selection previously made.
Button that resets the colors of all links.
Home button that will reload the initial network (nodes and links). However, previous selections made through the side menu will be kept, allowing the user to re-use previous selections but in the full matrix.
Filter button, which filters the current selection and displays all currently selected plasmids/nodes or all currently selected plasmids/nodes and all their linked plasmids/nodes (as well as the respective links). This may be particularly handy to filter queries.
Download button, that enable users to download the currently selected plasmids. This will download the queried accession numbers to a file named
pATLAS_download_<random_hash>.fas. For more on this subject, see Download api. NOTE: Some browsers may prevent pATLAS from opening new tabs or popups. Downloads will be blocked if the user doesn't allow pATLAS to open popups.
Table button, that opens a table with information available for the currently selected plasmids/nodes.
Statistics button, that will open a bar plot with the species present in the current selection. This will also allow access to all other statistic plots through the statistics popup (for further details see Statistics.
Heatmap button will generate a heat map that allows to compare multiple mapping or mash screen or even sequence results (for more details on how to import results go to here).
A slider that enables the user to search for a specific accession number or plasmid name (depending on the state of the slider). Then users may give a name or accession number to the form on the left (11th button in this image).
A search form in which users may search for a specific accession number or plasmid name, as mentioned before.
A button to submit the queried accession number or plasmid name (written in 11).
A button that clears the form in 11.