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- Click Finish from the t-SNE dialog to run t-SNE with the default settings
A t-SNE task node will be generated (Figure 2).
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The t-SNE plot is in 3D by default. You can rotate the 3D plot by lefleft-clicking and dragging your mouse. You can zoom in and out using your mouse wheel. The 2D t-SNE is also calculated and you can switch between the 2D and 3D plots using the Plot style radio buttons.
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In Partek Flow, we can color cells by more than one gene. We will now add a second glioma marker gene, GPM6A.
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Once cells have been classified, the classification is added to the Classifications section of the panel. The number of cells belonging to the classiciation classification is listed; in MGH42, there are 413 glioma cells (Figure 14).
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The pipeline view will open and the Classify cells tasks will run, generating a Classified groups data node (Figure 18).
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- Select the Filtered counts data node
- Select t-SNE from the Exploratory anlaysis analysis section of the task menu
- Select Configure on the t-SNE dialog (Figure 19)
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Once the task has completed, we can view the plot.
- Select the green t-SNE plot node
- Select Task Report from the task menu
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- Click Classify selection
- Name the classification Microgliaclassification Oligodendrocytes
- Click Save
- Deselect by double clicking on any black space on the plot
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