Spells

Spells provide reusable configuration snippets for datavzrd. These spells simplify the process of creating reports by allowing users to define common configurations in a modular way. Users can easily pull spells from local files or remote URLs, facilitating consistency and efficiency in data visualization workflows.

Below is a list of all the available spells in the datavzrd-spells repository. For adding new spells, please see the instructions in the datavzrd-spells repository.

clin-sig

This spell visualizes the clinical significance, given in clinvar significance terms (https://www.ncbi.nlm.nih.gov/clinvar/) The values should be given in a column consisting of strings and separated by ‘,’

Example

render-table:
  columns:
    some clinical significance column:
      spell:
        url: v1.3.0/med/clin-sig

Authors

Benjamin Orlik

genomic-coordinates

This spell visualizes genomic coordinates in a structured and visually enhanced way. It formats the coordinates with color-coded pills for reference and alternate bases, making it easy to read and interpret genomic variant data. The values should be given in a column with the format “<chromosome>:<reference><coordinates><alternate>” (e.g., “6:G29942560A”).

Example

render-table:
  columns:
    some clinical column containing genomic coordinates:
      spell:
        url: v1.3.0/med/genomic-coordinates

Authors

Felix Wiegand

boolean

This spell visualizes boolean values via colored +/- symbols.

Example

render-table:
  columns:
    some boolean column:
      spell:
        url: v1.3.0/logic/boolean
        with:
          # specify which values should be interpreted as true or false
          true_value: "true"
          false_value: "false"

Authors

Johannes Köster

p-value

This spell generates a heatmap visualization to represent the distribution of p-values or statistical significance in data. The heatmap uses a linear color scale to map values to a gradient from green over white to organge. The significance_threshold (e.g., p = 0.05) - a boundary between statistical significance and non-significance - can be adjusted dynamically based on the context or dataset.

Example

render-table:
  columns:
    some p-value column:
      spell:
        url: v1.3.0/stats/p-value
        with:
          significance_threshold: 0.05

Authors

Johannes Köster, Felix Wiegand