binx plot

Generate publication-quality visualizations from GWAS results.

Synopsis

binx plot --input <FILE> --output <FILE> [OPTIONS]

Description

The plot command creates visualizations from GWAS output files, including Manhattan plots, QQ plots, and LD decay plots.

Required Arguments

Argument	Description
`--input <FILE>`	Input file: GWAS results CSV (manhattan/qq) or genotype TSV (ld)
`--output <FILE>`	Output file path (.svg or .png)

Options

Option	Default	Description
`--plot-type <TYPE>`	manhattan	Type of plot: manhattan, qq, or ld
`--model <MODEL>`	-	Filter to specific genetic model
`--threshold <FLOAT>`	5.0	Significance threshold as -log10(p)
`--suggestive <FLOAT>`	3.0	Suggestive threshold as -log10(p) (0 to disable)
`--theme <THEME>`	classic	Visual theme
`--width <INT>`	1200	Plot width in pixels
`--height <INT>`	600	Plot height in pixels
`--title <TEXT>`	-	Plot title
`--chromosomes <LIST>`	-	Filter to specific chromosomes (comma-separated)

Threshold Recommendation: For accurate significance thresholds, use the value calculated by binx gwas --threshold or binx threshold. These commands compute thresholds using Bonferroni correction, M.eff (effective number of tests), or FDR methods appropriate for your dataset.

Plot Types

Manhattan Plot

Classic GWAS visualization showing -log10(p) across chromosomes:

binx plot \
  --input results.csv \
  --plot-type manhattan \
  --threshold 5 \
  --output manhattan.svg

Beta Feature: When --model is not specified, all models from the results file are plotted together with different colors. This multi-model visualization is currently in beta.

QQ Plot

Quantile-quantile plot for assessing genomic inflation:

binx plot \
  --input results.csv \
  --plot-type qq \
  --model additive \
  --output qq.svg

The plot includes:

Expected vs observed -log10(p)
95% confidence band
Diagonal reference line for visual inflation assessment

Beta Feature: When --model is not specified, all models from the results file are plotted together with different colors. This multi-model visualization is currently in beta.

LD Plot

Linkage disequilibrium decay over distance:

binx plot \
  --input geno.tsv \
  --plot-type ld \
  --ploidy 4 \
  --output ld_decay.svg

Important: LD plots require genotype data (dosage matrix), not GWAS results. The input file must have the format: marker_id, chr, pos, sample1, sample2, ... where sample columns contain dosage values. If you accidentally use a GWAS results file, all r² values will appear as 1.0 because the statistical columns are misinterpreted as samples.

LD plot specific options:

Option	Default	Description
`--ploidy <INT>`	-	Ploidy level (required for LD plot)
`--r2-threshold <FLOAT>`	-	R² threshold to mark on plot
`--max-pairs <INT>`	10000	Maximum marker pairs to sample
`--max-loci <INT>`	-	Maximum markers per chromosome
`--n-bins <INT>`	50	Number of distance bins for smoothing

Themes

Theme	Description
`classic`	Blue/orange alternating chromosomes (default)
`nature`	Muted gray tones for publication
`colorful`	Multi-color distinct chromosomes
`dark`	Dark background for presentations
`high_contrast`	High contrast for accessibility

Examples

Basic Manhattan Plot

binx plot \
  --input gwas_results.csv \
  --plot-type manhattan \
  --output manhattan.svg

Styled Manhattan Plot

binx plot \
  --input gwas_results.csv \
  --output manhattan.svg \
  --plot-type manhattan \
  --model additive \
  --threshold 7.3 \
  --theme nature \
  --title "Yield GWAS - Additive Model"

QQ Plot for Model Comparison

# Generate QQ plots for each model
for model in additive general 1-dom-alt; do
  binx plot \
    --input gwas_results.csv \
    --output qq_${model}.svg \
    --plot-type qq \
    --model $model
done

LD Plot with Threshold

binx plot \
  --input geno.tsv \
  --output ld.svg \
  --plot-type ld \
  --ploidy 4 \
  --r2-threshold 0.2

LD Plot for Specific Chromosomes

binx plot \
  --input geno.tsv \
  --output ld.svg \
  --plot-type ld \
  --ploidy 4 \
  --chromosomes chr05,chr09

Multi-panel Figure

# Create individual plots, then combine externally
binx plot --input results.csv --output manhattan.svg --plot-type manhattan
binx plot --input results.csv --output qq.svg --plot-type qq

Output Formats

The output format is determined by file extension:

Extension	Format
`.svg`	Scalable Vector Graphics (recommended)
`.png`	PNG raster image

Binx Documentation