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Rule sdge_visual

Purpose

Rule sdge_visual is designed to display the spatial expression of specific gene categories in colors red, green, and blue via spatula. NovaScope enables the visualization of >=1 gene sets. The gene categories for visualization can be defined in the config_job.yaml file (refer to Parameters).

Required Reference Files

Species-specific reference gene list files are required. By default, NovaScope provides precompiled gene lists for mouse and human. Users could provide their own custom gene list files.

If reference files are not available, the users could skip this visualization by setting action in drawsge as False (see details in Parameters section).

Input Files

  • Spatial Digital Gene Expression (SGE) Matrix and Associated Files The necessary inputs include a spatial digital gene expression (SGE) matrix, generated by Rule dge2sdge.

Output Files

The rule generates the following output in the specified directory path: 

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<output_directory>/align/<flowcell_id>/<chip_id>/<run_id>/sge/<run_id>.sge_visual

Description: A PNG file is created for each set of genes specified. By default, the spatial expression of non-mitochondrial genes, unspliced genes, and mitochondrial genes are depicted in red, green, and blue, respectively.

File Naming Convention: 

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<run_id>.<gene_type_in_red>_<gene_type_in_green>_<gene_type_in_blue>.png

The default visualization of non-mitochondrial gene, unspliced genes, and mitochondrial genes will be named as nonMT_Unspliced_MT.png.

File Visualization:

sge_image

Output Guidelines

It is recommended to review the spatial distribution of specified gene sets corresponds with the tissue area.

Parameters

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upstream:
  visualization:            ## specify the parameters for visualization
    drawsge:                ## specify the parameters for sdge visualization 
      action: True          ## specify whether to visualize the gene expression
      genes:                ## specify what sets of genes to be colored
        - red: nonMT        ## the first set of genes
          green: Unspliced
          blue: MT
    #   - ...               ## if more set of genes are required
      coord_per_pixel: 1000
      auto_adjust: true
      adjust_quantile: 0.99

  • The action Parameter Defaults to True. If False, NovaScope skips visualizing spatial expression for user-defined gene sets.

  • The genes Parameters NovaScope includes a selection of predefined gene lists with the following options: all (all genes); nonMT (non-mitochondrial genes); ribosomal (ribosomal genes); MT (mitochondrial genes); and nuclear (nuclear genes). To visualize additional specific gene groups, users can create gene list files (<prefix>.genes.tsv) in the directory specified in their config_env.yaml. Additionally, it is possible to visualize individual genes or groups of genes using specific names or regular expressions with spatula directly.

  • Other drawsge Parameters

    • coord_per_pixel specifies how many coordinates should be merged into one pixel. The default setting is 1000.0.
    • auto_adjust controls whether to automatically adjust the color intensity based on the maximum count. It is set to True by default.
    • adjust_quantile defines the quantile among non-zero pixels to use for auto-adjustment. The default value is 0.99.

Dependencies

Given the input from Rule dge2sdge serve as the input for sdge_visual, Rule sdge_visual can only execute if the input SGE is available or the dependent rules have successfully completed their operations. See an overview of the rule dependencies in the Workflow Structure.

Code Snippet

The code for this rule is provided in a06_sdge2sdgeAR.smk.