.. |sep| image:: /images/toolbar-separator.png .. |tb-nodes-mapping| image:: /images/toolbar-metadata-nodes-mapping.png :alt: Mapping Section of Nodes Table Toolbar .. |tb-nodes-nodes| image:: /images/toolbar-metadata-nodes-nodes.png :alt: Nodes Section of Nodes Table Toolbar .. |tb-nodes-tools| image:: /images/toolbar-metadata-nodes-tools.png :alt: Tools Section of Nodes Table Toolbar .. |reset-ordering| image:: /images/metadata-table-reset-ordering.png :alt: Upper Left Corner of Metadata Table .. |node-label| image:: /images/icons/node-label.svg .. |node-pie| image:: /images/icons/node-pie.svg .. |node-size| image:: /images/icons/node-size.svg .. |node-color| image:: /images/icons/node-color.svg .. |highlight-yellow| image:: /images/icons/highlight-yellow.svg .. |highlight-red| image:: /images/icons/highlight-red.svg .. |spectrum| image:: /images/icons/spectrum.svg .. |query| image:: /images/icons/library-query.svg .. |formula| image:: /images/icons/calculator.svg .. |cluster| image:: /images/icons/cluster.svg .. |remove| image:: /images/icons/list-remove.svg .. _metadata_tables: Metadata Tables =============== Nodes and edges tables will contains metadata. When nodes or edges are selected in a :ref:`Network View `, only those nodes/edges will appear in the corresponding tables. Filtering can also be performed using the :ref:`search toolbar `. These tables can be hidden/shown using the :menuselection:`View --> Toolbars` menu. They can also be moved to a different position in the main window or even detached from the latter by simply dragging it to the new position or double-clicking on it's title bar. .. image:: /images/view-data-menu.png :alt: Data menu .. note:: Columns can be selected via the |mouseright| right mouse button while the |mouseleft| left mouse button is used to change ordering. |reset-ordering| Default ordering can be reset by |mouseright| right clicking in the empty region on the upper left of the table (left side of the first column and above first line). .. _metadata_nodes: Nodes ***** The nodes table list all nodes and their associated metadata. There is a line per node and a column per metadata type. The first column of this table is always :guilabel:`m/z parent` and contains *m/z* ratios of ions loaded from the :ref:`import data dialog `. The second one is reserved to :guilabel:`Database search results`. This column will contain a list of standards found in the databases (See :ref:`Databases Query `). It is hidden by default and will be visible only if there is at least one results to show. .. _nodes_toolbar: Nodes Toolbar ~~~~~~~~~~~~~ |tb-nodes-mapping| |sep| |tb-nodes-nodes| |sep| |tb-nodes-tools| The toolbar located on top of the nodes table is divided in three sections. .. _nodes_toolbar_mapping: Mapping section --------------- |tb-nodes-mapping| The first section is dedicated to change how nodes are representated in :ref:`views `. Just select one or more metadata column(s), with a |mouseright| right click, then use one these buttons. The dropdown menu include a menu item to undo these changes. - |node-label| Use data from the selected column as labels for nodes in the :ref:`views `. - |node-pie| Represents the data in the selected columns in the form of pie charts on the nodes. - |node-size| Adjusts each node size based on the data from the selected column. - |node-color| Defines color of the nodes from the selected column data. .. _nodes_toolbar_nodes: Nodes section ------------- |tb-nodes-nodes| In this second section, you can interact with nodes and their associated MS/MS spectra: - |highlight-yellow| Highlight in the :ref:`views ` the nodes selected in the table. You can then use the :guilabel:`Zoom to the selected region` function (see :ref:`view_toolbar`) to easily locate these nodes. - |spectrum| Views the MS/MS spectrum associated to the selected node (shortcut :kbd:`S`). You can also compare this spectrum to the one associated to a second node using the :guilabel:`Compare spectrum` function accessible from the dropdown menu (shortcut :kbd:`C`). See :ref:`spectrum_view`. - |query| You can try to find similar spectra in databases by using this function. See :ref:`databases`. .. note:: Functions from this section are also accessible from a context menu that will pop up if you |mouseright| right click in a cell of the nodes table. .. _nodes_toolbar_tools: Tools section ------------- |tb-nodes-tools| The last section defines tools that will end up adding columns to the table: - |formula| This tool allows you to create new data columns by combining existing columns using mathematical functions. See :ref:`tools_formulae`. - |cluster| This one uses a clustering algorithm (HDBScan_) to find clusters in the visualisation and colorize nodes according to. See :ref:`tools_cluster`. - |remove| Not really a tool, but you can use it to remove unwanted columns from the table. .. _metadata_edges: Edges ***** The edges table list all edges and the nodes they link. This table has meaning only for the :ref:`classical network view ` as the other views don't use edges. There is a line per edge and the following columns are available: - Source: The first node that the edge link. Source and target are arbitrarily defined and this has no special meaning since the graph is not directed. - Target: The second node that the edge link. Same comment than the :guilabel:`Source` column. - Delta MZ: Difference of *m/z* ratio between the parent ions associated to the two nodes. Sign is irrelevant. - Cosine: The similarity score calculated to compare the spectra associated to the two nodes. Value lies between 0 and 1, the higher it is, the closer the spectra are to each other. - Possible interpretation: Possible interpretation of the :guilabel:`Delta MZ` based on the exact mass. Edges Toolbar ~~~~~~~~~~~~~ The toolbar on top the edges table offers a few functions. .. image:: /images/toolbar-metadata-edges.png :alt: Edge Table Toolbar - |highlight-yellow| Highlight in the :ref:`views ` the edges selected in the table. - |highlight-red| Highlight in the :ref:`views ` the nodes connected by the edges selected in the table. .. note:: These functions are also accessible from a context menu that will pop up if you |mouseright| right click in a cell of the edges table.