Condensed Quick-Start Example
The following guide presents a few quick examples of Explicet capabilities. For a more thoroughly documented example of the Explicet project process, please view the Explicet Tutorial.
- Open Explicet
- A pop-up window will open with several different options
Click Create Project
Enter Project Name, “Tutorial_HSM”, when prompted
Click OK
I. Import the OTU table.
File → Import → File → OTU Table Counts
- Select “Tutorial_HSM_OTU_2_Explicet”
Click Open
- Another pop-up window will open
Click Import
II. Import metadata for the OTU table.
File → Import → Metadata
- Select “Tutorial_HSM_Metadata”
Click Open
- Another pop-up window will open
Click Import
- Another pop-up window will open
Click Done
IV. Save the project.
Click Save button in upper right corner of current workspace window
- Enter desired file name (default file name is project name with an “_Explicet_Project” extension) and location
Click Save
V. Create a pie chart.
Tools → Plot → Pie Chart
- A new window will appear with the hierarchical data available in the workspace
- Holding “Shift”, select all of the phyla (Acidobacteria through Verrucomicrobia)
Click Add to Pie
Click Plot
- A new window will appear containing pie chart display options
To display a single pie chart that includes all libraries’ data, select the 30 Total Libraries checkbox
Click OK to view the pie chart
Click Done to return to the pie chart setup window
Click Save As Figure in lower right corner of window
- Enter desired figure name
Click OK
Click Done to return to the main project window
(The figure can always be recalled by clicking Figures button in the upper right corner of workspace window)
VI. Create a workspace (a subset of libraries and OTU lines).
File → New → Workspace
- Enter “Back” workspace name when prompted
Click OK to create the new workspace
Data → Select Libraries
- New pop-up window appears for creation of filters
Click New on far right side of window
- Enter “Back” filter name when prompted
Click OK
- “Back” appears in upper left corner of window
Click Add on right side of upper pane
- Use the first pull-down menu to select “Anatomy” (metadata to filter by)
- Use the second pull-down menu to select filter “contains” (operator)
Enter “back” into Value
To apply filter, click Select in upper right corner of window
Click Save Filter on far right side of window to keep the filter
Click Done
- The workspace now only displays libraries sampled from the back.
VII. Compute beta-diversity (heatmap of Morisita-Horn matrix).
Tools → Analyze → Beta Diversity → Morisita-Horn
- A new window appears containing a comparison matrix with the calculated Morisita-Horn similarity values
Click Plot on lower right side of window
- A heatmap appears displaying a comparison of the OTUs between the “back” library samples
Click Done to return to the heatmap setup window
Click Save As Figure in lower right corner of window
- Enter desired figure name
Click OK
Click Done to return to the main project window
(The figure can always be recalled by clicking Figures button in the upper right corner of workspace window)
VIII. Create a Collector's Curve of Species observed, Sobs.
Tools → Analyze → Alpha Diversity
- A new pop-up window will appear
To create curves, deselect Single statistic at Rarefaction point only
To create smooth curves, change Bootstrap Size to 1000
Click Bootstrap
Click Plot on lower right side of window
- A pop-up will appear with all the diversity measures and library names
Select Sobs (the number of OTUs observed in a library)
Click OK
- A plot of the rarefaction curves for the selected measures and libraries will appear
Click Done to return to the alpha diversity setup window
Click Save As Figure in lower right corner of window
- Enter desired figure name
Click OK
Click Done to return to the main project window
(The figure can always be recalled by clicking Figures button in the upper right corner of workspace window)