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SubtitleText Selecting malignant cells AnchorName Selecting malignant cells
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The number of selected cells is indicated in the Selection section of the menu.

• Select Classify selection (Figure 14)
  
  

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SubtitleText Classifying selected cells AnchorName Classifying cells
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A dialog to give the classification a name will appear. 

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SubtitleText Classifying selection AnchorName Classifying cells
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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 is listed; in Astrocytoma 2, there are 253 malignant cells (Figure 15). 

 

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SubtitleText The number of cells in each classification is displayed in the classification section. AnchorName Viewing classifications
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Classifications made on the t-SNE plot are retained as a draft until you exit the t-SNE task report. The Save classifications button runs a task, Classify cells, which generates a new Classified cells data node. In this tutorial, we will classify malignant cells for each sample before we save the classifications, but if necissary, you can run Classify cells for one sample, exit the t-SNE task report, and continue classifying the next sample later starting with the Classified cells data node. 

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SubtitleText Classifying malignant cells AnchorName Classifying cells
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• Select Classify selection 
• Type Malignant or select Malignant from the prompt (Figure 17)
• Select Save
  
  

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SubtitleText Adding cells in a second sample to an existing classification AnchorName Classifying cells as an existing classification
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• Repeat these steps for each of the 5 6 astrocytoma and 3 4 oligodendroglioma samples

Once all samples have been classified, it is useful to check the number of cells in each sample assigned to each classification. 

• Select Classification summary Summary (Figure 18)
  
  

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SubtitleText Navigating to the classification summary AnchorName Navigating to classification summary
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The classifications summary lists every sample, the number of cells in the sample, and the number of cells in each classification, and the percentage of cells in each sample that belong to each classification (Figure 19).

 

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SubtitleText Viewing the classification summary AnchorName Classification summary
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With the malignant cells in every sample classified, it is time to save the classifications.

• Select Save Click Apply classifications 
• Select Save Apply when asked to confirm

The pipeline view will open and the Classify cells tasks will run, generating a Classified groups data node (Figure 20).

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SubtitleText The Classify cells tasks generates a Classified groups data node AnchorName Classify cells task
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One multi-sample t-SNE plot

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• Select the Single cell data data node
• Select t-SNE from the Visualizations Exploratory anlaysis section of the task menu
• Select Configure on the t-SNE dialog (Figure 21)
  
  

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SubtitleText Accessing the t-SNE advanced options AnchorName Accessing advanced options
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• Deselect Click the Split cells by sample option under MiscSelect  Misc to uncheck it
• Click Apply (Figure 22)
  
  

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SubtitleText Setting t-SNE to plot all samples together AnchorName Setting t-SNE to plot all samples together
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•  Select  Click Finish to run the t-SNE task

The t-SNE task will be added as a new green layer in the analysis tab (Figure 23).

 

 

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SubtitleText All samples t-SNE task is added as a new layer AnchorName t-SNE task new layer

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