Nearly all of the information derived from SeqGeq can be exported for publication or further downstream analysis.
To export populations select the population nodes of interest, right clicking on one of those populations, and selecting “Export/Concatenate”:
Within the resulting dialog users can select between exporting individual populations, or combining (aka “Concatenating”) subpopulations together. This dialog also allows for the selection of parameters to include in the export, the format of the export, and the export location.
Combining sub-populations, or samples will result in the creation of a SampleID categorical parameter which distinguishes between samples combined by integer values corresponding to the order of samples combines.
Note: The 6K_PBMC.csv file is actually a concatenation of 5 samples of different sizes. Try running the AutoGateCategorical plugin (see Chapter 8 – “Clustering” for guidance there) on the “SampleID” parameter do distinguish between samples there.
Statistics can be generated within the SeqGeq workspace by selecting a population of interest and choosing “Add Statistics”:
To export these statistics for the workspace, click on the SeqGeq icon, and select the XLS option within the Export Workspace dialog there:
There are a number of options for exporting Genesets from SeqGeq:
Export option within the Genes tab:
Figures can be exported from SeqGeq via the Layout Editor. The layout’s figures also enhance some of the analyses possible from the platform. To add figures to the layout simply open the Layout Editor, then drag and drop a population of interest from the Workspace directly into the Layout. This will create a figure illustrating the last set of parameters viewed for that population in the Graph Window.
Adjustments to these figures can be accomplished by double-clicking on them to bring up the Graph Definition window, where a variety of different settings are available:
Other figure formatting options can be found in the Object tab of the Layout Editor:
Try creating an overlay of K-Means clusters within the Layout editor on tSNE parameters. To create an overlay, simply drag populations of interest on top of one another within a Layout:
Note: PNG and JPG figures from 3rd party applications can also be added directly to SeqGeq’s Layouts by dragging and dropping. This is frequently done automatically by plugins in SeqGeq which utilize R packages.
Saving a SeqGeq workspace creates a GeqZip file folder, which can be loaded into SeqGeq in order to load the saved workspace. However, this ZIP file also contains all of the artifacts generated during the course of an analysis, including Geneset Libraries, the raw data file itself, and XML copy of the workspace, any images added to the layout editor, and much more:
This means you can open the GeqZip by unzipping it and investigate the contents as desired. This also makes the analysis very easy to share with collaborators or for publication of the work completed.
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