Visualize the annotated image from the automatically generated Spatial report task

With samples imported and annotated, we can begin analysis. 

• Click Analyses to switch to the Analyses tab

For now, the Analyses tab has only a single, circular node, Single cell counts. As you perform the analysis, additional nodes representing tasks and new data will be created, forming a visual representation of your analysis pipeline. A Spatial report task result node (rectangle) is also automatically generated for this type of data. 

• Click the Spatial report node
• Click Task report on the task menu 

The spatial report will display the first sample (Replicate 1). We want to visualize all of the samples using the steps below. 

• Duplicate the plot by clicking the Duplicate plot button in the upper right controls (arrow 1)
• Open the Axes configuration option (arrow 2)
• Change the Sample on the duplicated image under Misc (arrow 3)

Each data point is a tissue spot. Duplicate and change the sample to view multiple samples. 

Visualize the annotated image from the Annotate Visium image task

If starting with fastq files, the Annotate Visium image task will create a new result node, Annotated counts. 

• Double click on the Annotated counts node to invoke the Data Viewer showing data points overlaid on top of the microscopy image 
• Follow the steps outlined above by duplicating the image to visualize the multiple samples

Data Viewer session as a result of opening an Annotated counts data node. Follow the same three steps outlined above to duplicate and view multiple sample images. 

Modify Style

To modify the points on the image to show more of the background image use the Style configuration option. 

• Press and hold Ctrl or Shift to select both plots 
• Click Style in the left panel
• Move the Opacity slider to the left
• Change the Point size to 3 

• Click Save in the left panel and give the session an appropriate name

Modify Axes

• Click Axes in the left panel
• Toggle off Show lines for both the X & Y axis
• Toggle off Show title and Show axis for both the X & Y axis

Color by gene expression

• Click Style
• Click the blue circle node to the right of the Color by drop-down
• Select the Normalized counts node
• Choose to Color by Numeric triad
• Use the Green drop-down to select IL32, Red drop-down to select DES, and Blue drop-down to select PTGDS gene expression

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