In viewpoly: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species

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

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.