Select Data
A. Select Libraries
This function allows the user to select subsets of libraries via library names (or portions of library names), metadata, and/or specific OTUs. Library selection is often used in conjunction with workspaces to enable analysis of subsets of data within a project. A workspace may have ONE current filter; to create a new subset, a new workspace with a different current filter must be created. This is usually accomplished by creating a new workspace using the Clone Workspace button, then creating or choosing a filter that selects only the libraries needed for the experiment to be performed.
Data → Select Libraries
- New pop-up window appears for creation of filters
Click New on far right side of window
- Enter desired filter name when prompted
Click OK
- Filter name will appear in upper left corner of window
- The popup window has three panes. The upper pane is for creating filters based on metadata and library names (column filter), and the middle pane is for selecting OTUs (row filter)...
1. Create a Library or Metadata Filter (Column Filter)
Click Add on right side of upper pane
- Use the first pull-down menu to select metadata to filter by
- Use the second pull-down menu to select filter operator
If one criterion does not include all the desired libraries, select Add again
Another criterion can be added to the filter using the And/Or function.
To apply filter, click Select in upper right corner of window
When the Select button is clicked, the number and names of libraries fitting the criteria of the filter will be displayed at the bottom of the popup window.
Click Save Filter on far right side of window to keep the filter
2. Create an OTU Filter (Row Filter)
Click Add on right side of middle pane
- Type in the OTU name you wish to filter by (any level of the hierarchy)
- Use the first pull-down menu to select whether to filter by OTU name or member count
- Use the second pull-down menu to select filter operator
The Select OTU Group Name button is useful when the operators is in OTU Group or is not in OTU Group are selected. Often, OTU Group names are very long and complicated. By clicking the Select OTU Group Name button, a list of OTU Groups will appear. Click on the desired OTU Group name, then click Select, and the OTU Group name will be copied to the clipboard. Then, place your cursor in the neighboring Value text box and click Ctrl-v to paste the name.
Multiple OTUs can be filtered by using Add function
Another criterion can be added to the filter using the And/Or function.
To apply filter, click Select in upper right corner of window
- When a selection is made, the number of libraries and the library names, and the number of hits in the selected OTU will be displayed at the bottom of the popup window.
Click Save Filter on far right side of window to keep the filter.
The way to think about how library selection and OTU selection work together is that FIRST a library is selected with the Metadata Selection Criteria rules, and then SECOND the OTUs for inclusion within a selected library are chosen with the Taxonomy Selection Criteria filter. In other words: OTU selection filters do not select or influence the selection of libraries; they only select the OTU values to be retained within libraries that are selected by the Metadata Selection Criteria.
3. Change Current Filter
- Click the radio button next to the filter name in the top of the workspace window
- Click on the current filter name
- Select a different filter from the drop-down list
- Note: If a filter is changed in a workspace, all figures associated with that workspace will be affected.
4. Rename Filter
- There are 2 different ways to rename a filter:
1. Data → Select Libraries
Click Rename on right side of window
- Type over existing name in the pop-up window
Click OK to rename filter
2. Make sure the radio button next to the Current Filter on the workspace window is not selected
- Type over the existing filter name in the dialog box
B. Group Data
Explicet allows the data making up multiple libraries to be combined by averaging the relative abundances of included OTUs. To reiterate: libraries created via the Group Libraries command in Explicet are created by AVERAGING THE RELATIVE ABUNDANCES (% of Library) of each OTU found within the libraries selected - NOT by merely summing the counts per OTU per library included in a group. For example, one might want to compare all libraries obtained by sampling within a building (Group 1) with all libraries within the study resulting from outdoor samples (Group 2). Explicet assumes that a library is the set of results that represent all taxonomic results from a single sample. To combine libraries without introducing a bias associated with large differences in within-group library sample sizes, Explicet combines libraries by averaging the relative abundances for each OTU in each library included in a group. In Explicet, when grouped libraries are displayed as “counts”, the Counts displayed are computed backwards from the averaged percent abundances for each taxon. Results for the OTUs, especially for those OTUs with small number of counts, or OTUs whose counts vary widely between the grouped libraries, may be higher or lower than one expects from knowing the raw sums of the counts that went into the groups. Users need to be aware of the statistical implications of any operations performed on grouped libraries, as the operations are performed on the averaged relative abundances, or imputed sequence counts, rather than the raw sequence counts.
1. Group Libraries
- This function allows the user to assemble libraries into a larger category by shared metadata features (e.g., multiple libraries from the same patient or from multiple sites of the same chemistry).
Group → Group Libraries
- A pop-up window will open
- In left panel, select the metadata descriptor you wish to group by
Click Add button between panels
- Name of metadata descriptor will appear in the right panel
For metadata that are numbers, a bin size can be specified by clicking on the number in the Bin Size column and entering the desired size. For example, age metadata can be binned by 5, resulting in group names like 0-5, 5-10, 10-15.
Click Group at top right of window to accept grouping
In the main workspace, make sure the Show Lib Groups check box is selected. Columns should now have metadata groupings rather than library names.
a) Remove Metadata Group
If you wish to remove a metadata grouping, follow the same procedure, except select the undesired descriptor in the right panel and click Remove button between panels.
2. Group OTUs
Often it is desirable to use a more basal taxonomic category than that provided by the employed sequence classification software. This is easily done in Explicet by forming a new taxonomic category combining several individual categories. Explicet does not restrict the taxonomic categories that are combined, meaning any OTU name can be combined with any other OTU name (user beware). For instance, the group function can be used to create an arbitrary “Other” taxonomic category consisting of disparate OTUs. Grouping taxonomic categories is done within the OTU pane. Combining OTUs is performed by Explicet by summing the raw counts of all of the OTU lines selected for the group. Group OTU simply adds the raw counts together for each item in the group, UNLIKE Group Libraries.
There are two components to grouping OTU names: OTU Groups and OTU Rule Sets. Multiple OTU Groups, or a single OTU Group, may make up one OTU Rule Set. Every OTU Group must be part of an OTU Rule Set. Therefore, when creating a new OTU Group in a workspace, the user is required to create a new OTU Rule Set. Once an OTU Rule Set is established in a workspace, the user can add new OTU Groups or edit the existing ones in the current OTU Rule Set.
a) Create OTU Group and OTU Rule Set
- Select the OTUs to combine
- Several OTUs can be selected by clicking the first OTU, then Shift-click on the last OTU.
- Non-sequential OTUs can be selected (or deselected) via Ctrl-click.
- Select a single OTU line to create a consistent grouping rule, such as grouping all OTUs that start with the same name.
Group → Group OTU
- A new window appears
Enter desired OTU Rule Set Name in the top field
- In a workspace that already has an active OTU Rule Set, the OTU Rule Set Name cannot be edited. Adding a new group simply creates a new OTU Group within the current OTU Rule Set.
The next field shows the Selected OTU Names that will be added to the group
- To edit the OTU names shown, double click on the name. For example, if "Bacteria/Acidobacteria/Acidobacteria/Candidatus-Chloracidobacterium" is selected, and you want to work with all OTU names of the Acidobacteria phylum, double click on "Bacteria/Acidobacteria/Acidobacteria/Candidatus-Chloracidobacterium" to edit it, and delete everything except for "Bacteria/Acidobacteria/".
- Identify the group to which the OTUs will be added
To create a new OTU Group for the selected OTUs, select Create a new OTU Group containing…, and enter the new OTU Group name in the text box to the right.
To add the OTU names to an existing OTU Group, select Add the Selected OTU Names to an existing OTU Group named, and choose the desired OTU Group name from the drop down menu.
- Identify how the selected OTU names should be used
When the OTU names are added to the OTU Group specified above, should Explicet place only the exact OTU names shown into the group? If so, select Exact Match.
Or, if you selected one OTU name, or maybe an abbreviated OTU name, and you'd like all OTU names that begin with that same text to be added to the group, then choose Starts With.
Click Save
- The pop-up will disappear
- The OTU Group appears alphabetically in the OTU table (its members removed from the table)
- When OTUs are grouped, OTU names included in the group can be viewed by hovering your cursor over the group name shown in the OTU pane.
OTU groupings are available in the OTU Heatmap and OTU Stacked Bar functions, but not in the Pie Chart function. Any and all OTU Groups that are created will be carried forward into the analyses performed, and graphics created, within any workspaces employing the newly modified OTU Rule Set.
Note: One item OTUs (such as OTU Group names or OTUs that can only be traced to domain level, like “Bacteria”) are considered the last OTU position; single name OTUs will disappear when OTU Show Last is deselected.
For information on exporting OTU Rule Sets, see Import/Export Workspace Rules.
- Select the OTUs to combine
b) Add Single OTU Name to Existing OTU Group
- Select the OTU to be added
Group → Group OTU
Select Add the Selected OTU Names to an existing OTU Group named:
- Choose the desired OTU Group name from the drop down menu
Select Exact Match
Click Save
- The individual OTU name will be removed from the OTU table and added to the OTU Group
- Note: Although single OTU names can be added to an existing OTU Group, two or more OTU Groups cannot be grouped. To accomplish the equivalent effect of grouping the two OTU Groups, create a new OTU Rule Set that puts the desired constituent OTUs into a single OTU Group.
c) Remove OTU Group
- Select the group name in the OTU table
- If nothing is selected, all groups in the OTU table will be ungrouped.
Group → Ungroup OTU
- A new window appears
Click Save to simply remove the OTU Group from the current OTU Rule Set.
Click Save As to make no changes to the original OTU Rule Set while also saving a copy of the current OTU Rule Set without the selected OTU Group; if the user clicks Save As, a pop-up will appear for entering a new OTU Rule Set Name. The new OTU Rule Set becomes the OTU Rule Set assigned to the workspace. The name of the current OTU Rule Set assigned to the workspace is displayed in the title of the OTU pane on the workspace window.
- Group name is removed from the OTU table; its members are re-added to the table
- Select the group name in the OTU table
d) Remove OTU Names from Existing OTU Group
- Select the group name in the OTU table
Group → Remove OTU Names from OTU Group
- A pop-up will appear with a list of OTU names within the OTU Group
- Select the OTU names to be removed
Click Remove
Click OK
- The OTU name will be removed from the OTU Group and added back to the OTU table
e) Rename OTU Group
- Select the group name in the OTU table
Group → Rename Group
Enter new OTU Group Name where prompted
Click OK
f) Edit OTU Rule Sets
Group → Edit OTU Rule Sets
A window will appear with a list of all available OTU Rule Sets
Select the OTU Rule Set of interest
- There are several different ways to view an OTU Rule Set definition:
1. Click View
- 2. Double-click on an OTU Rule Set name
- 3. Ctrl-click the magnifying glass button on the OTU pane.
4. To view an OTU Rule Set definition and its members: simply left-click the magnifying glass button on the OTU pane to view both the definition and a list of the OTU Group members within the workspace in which the button was clicked.
Click Merge to join multiple OTU Rule Sets. Using Shift-click or Ctrl-click, the user can select two or more OTU Rule Sets from the OTU Rule Sets column, and then click Merge. A pop-up window will appear for creating a new name for the merged OTU Rule Set; OTU Rule Sets will be combined into a new OTU Rule Set, however, the original/individual OTU Rule Sets will still remain in the list.
Click Delete to remove an OTU Rule Set from the project.
Click Rename to change the name of an OTU Rule Set.
Click Save As to keep the current OTU Rule Set and also create a copy of the OTU Rule Set (after prompting the user to enter a new OTU Rule Set name).
g) Workspace OTU Rule Set Manager
- This function provides a simple way of managing which OTU Rule Sets are applied to which workspaces. The user can assign only one OTU Rule Set to each workspace, but multiple workspaces can have the same OTU Rule Set.
Group → Workspace OTU Rule Set Manager
- A window will appear with two columns
- The list of workspaces, on the left, is static and un-editable. The column of OTU Rule Sets, on the right, consists of drop-down selectors with all possible OTU Rule Set options next to each workspace.
Adjust which OTU Rule Sets are applied to each Workspace as desired
Click OK