A drupal module for eQTL signals and LD matrix visualization in ZEAMAP.
Find a demo here: DEMO
The gene-eQTL bubble heatmap visualization script in this module were modified from GTEx Gene-eQTL Visualizer.
- Drupal 7.x
- Tripal 7.x-3.x
Download this repository, switch to drupal environment, and lunch this module with
drush en -y zmap_eqtlviz
Once the module was correctly loaded, it would create four tables to store necessary information for Gene-eQTL in ZEAMAP in the PostgreSQL database. These tables could also be manually created through includes/zmap_eqtlviz.sql. The related Gene-eQTL information should be imported to these tables using sql command accordingly.
In order to display the LD matrix, this module would search for Pairwise LD score files in the drupal public dir (sites/default/files) with the gene_id as prefix and "LD" as suffix. So please make sure the related pairwise LD files were correctly prepared. The LD file should be tab-separated files with format below.
# pairwise LD file format (no header)
<variant1> <variant2> <LD_r2>
# example:
chr5.s_209839785 chr5.s_209839821 0.4060
chr5.s_209839785 chr5.s_209839830 0.3034
chr5.s_209839785 chr5.s_209839926 0.3581
chr5.s_209839785 chr5.s_209839951 0.3547
chr5.s_209839785 chr5.s_209840008 0.3304
chr5.s_209839785 chr5.s_209840012 0.3487