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.
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.
Modify Style
To modify the points on the image to show more of the histology 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
Additional Assistance
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
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