## HIDECAN - Parameters Description

### Select Dataset

**Track Selection**:
- Choose which GWAS, DE, or CAN dataset to visualize
- Multiple datasets can be loaded simultaneously
- Switch between datasets to compare results

**Filter by Chromosome**:
- Display all chromosomes or select specific ones
- Useful for focusing on candidate regions
- Reduces visual clutter
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### Score Thresholds

**Significance Cutoff**:
- Set minimum score for displaying associations
- Higher thresholds = more stringent filtering
- Default based on significance threshold (e.g., -log10(p-value) > 3)
- Interactive slider allows real-time adjustment

#### HIDECAN plot options

- Title: Customize plot title
- Subtitle: Add subtitle for context
- Number of rows: Adjust number of rows in the plot layout
- Number of columns: Adjust number of columns in the plot layout
- GRaphic height: Adjust height of the plot
- Legend position: Choose where to place the legend (top, bottom, left, right)
- Point size: Adjust size of points in the plot
- Font size: Adjust size of text in the plot
- Label size: Adjust size of labels in the plot
- Label padding: Adjust spacing around labels
- Add custom prefix for your 3 tracks: Enter a prefix to distinguish your tracks

Select:
- Colour genes by score? If yes, the points will be coloured according to their score value. If no, all points will be the same colour.
- Remove empty chromosomes? If yes, chromosomes with no significant hits will be removed from the plot. If no, all chromosomes will be displayed regardless of significance.
- Remove empty traits? If yes, traits with no significant hits will be removed from the plot. If no, all traits will be displayed regardless of significance.

### Additional Resources

**HIDECAN Documentation**: [https://plantandfoodresearch.github.io/hidecan/](https://plantandfoodresearch.github.io/hidecan/)

**GWASpoly Tutorial**: [https://potatobreeding.cals.wisc.edu/software/](https://potatobreeding.cals.wisc.edu/software/)

**VIEWpoly Tutorial**: [https://cristianetaniguti.github.io/viewpoly_vignettes/](https://cristianetaniguti.github.io/viewpoly_vignettes/)

**Tools for Polyploids**: [https://www.polyploids.org/](https://www.polyploids.org/)
