View tissue images
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Partek
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With the pre-processed samples imported, we can begin analysis.
Click Analyses to switch to the Analyses tab
For now, the Analyses tab has a starting node, a circular node called Single cell counts and also a rectangular task node called Spatial report which was automatically generated for this type of data. As you perform analyses, additional nodes representing tasks and new data will be created, forming a visual representation of your analysis pipeline.
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.
If starting with unprocessed 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
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 the axes to remove the X and Y coordinates from the tissue image.
Press and hold Ctrl or Shift to select both plots
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
Style the image and color by normalized gene expression using three genes of interest.
Press and hold Ctrl or Shift to select both plots
Click Style
Select the Normalized counts node as the source
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 genes (type in name of gene in drop-down)
Increase the Point size to 11
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Click the blue circle node to the right of the Color by drop-down
To color by the which we previously determined in this tutorial, use the Color by drop-down and select Cell Type. Cell type is a blue categorical attribute while green attributes are numerical.
