Main Window Overview
The main window of Explicet has three parts (from top to bottom):
1.
The classic graphical user interface pull-down menus consisting of File, Edit, Data, Group, Tools, View, and Help.
2. The command and control cluster, used to display and select the options in effect for a project and workspace.
3. One or two data display panes.
The command and control cluster is organized into 7 columns (from left to right):
1.
The Project / Workspace / Current Filter column displays the name of the dataset, the name of the current workspace, and the name of a filter that can be used to select libraries within that workspace. Note that the workspace line ends with a radio button that, if clicked, converts the text box into a drop down menu that allows the user to open or move to any workspace within the project.
2.
Selects which data display panes (described below) are displayed: Hierarchy, OTU, or Both.
3.
Selects how the data are displayed within the Hierarchy and OTU panes. Data can be displayed as Counts, % of Library (a.k.a. percent abundance), and % of Total.
4.
Allows the user to interactively control the detail in which OTU names are displayed within the OTU pane. OTU Start selects the first taxonomy category (counting from 1) to be shown. OTU Width determines the maximum number of categories shown. The check box, OTU Show Last, can optionally force the terminal category of an OTU name to always be shown independent of the state of OTU Start and OTU Width. Setting OTU Width to zero, and checking OTU Show Last, causes display of only the terminal category for each OTU name.
5.
Hierarchy Level controls the default number of levels that are expanded in the Hierarchy column of the Hierarchy pane.
6.
This column controls how library data are to be displayed in the Hierarchy and OTU panes. It also contains a Notes button for recording workspace notes and ideas.
Show Libraries diplays all of the active libraries in a workspace.
Show Sorted Libs displays all libraries in a workspace after sorting and annotating library names by metadata selected through the View → Sort Libraries function.
Show Lib Groups shows the groups active and selected by the Group → Group Library function.
7.
The four buttons in the seventh column (from top to bottom) allow the direct selection of figures created in any workspace in the project (Figures), a one click creation of a new workspace from the current workspace (Clone Workspace), a one click Save of all data within a project, and a one click shutdown of all workspaces in a project via Close Project (the user is first prompted to save any unsaved modifications to the project). All active windows closed by Close Project will be re-opened exactly as shown when the project is re-started.
Data display panes
1.
The Hierarchy Pane: This pane allows the user to explore a data set in terms of hierarchical levels by which the user has organized the sequences, such as Domain, Phylum, Class, Order, Family, Genus, and Species. These categories are classifier dependent and need not be phylogenetic/taxonomic classifications (e.g., for non-16S rRNA datasets). This pane shows a hierarchical summary of the data imported into the project, with levels selected as rows on the left side of the pane. Initially, data are presented as sequence counts for particular taxonomic levels, displayed for all libraries (the column “Total”) or broken down library by library.
2.
The OTU Pane: The left side of this pane shows an alphabetical list of all of the OTUs found in the data selected for the workspace. The “Total” column shows the sum of sequence counts (or average percentage) in each OTU of all samples, and the rest of the pane presents data for individual libraries. This pane displays the data that will go into the analysis functions of Explicet or other statistical tools such as SAS or R via the Export → OTU function.
When clicked, this button will open a window that describes the current OTU Rule Set and lists the workspace members included in that rule set.