credtools plot

Create plots from QC or fine-mapping outputs.

credtools plot INPUT_PATH [OPTIONS]

Common Use

credtools plot results/locus_1 \
  --type summary \
  --output results/locus_1/qc_summary.png

Options

Option	Meaning	Default
--type	plot type; auto-detected if omitted	none
--output	output path, such as PNG, PDF, SVG	none
--width	figure width in inches	16
--height	figure height in inches	12
--dpi	output DPI	300
--include-upset	include SNP missingness upset plot	on

Plot Types

summary
locus_qc
locusplot
lambda_s
maf_corr
lambda_s_outliers
dentist_s_outliers
locus_pvalues
zscore_qq
ld_decay
ld_4th_moment
snp_missingness

Examples

credtools plot qc_results --type summary --output qc_summary.png
credtools plot results/locus_1 --type locusplot --output locusplot.pdf
credtools plot results/locus_1 --type snp_missingness --output missingness.svg