Spells | Datavzrd v2.58.0 documentation (original) (raw)

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.

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

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 “:” (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

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

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