ZEAMAP GWAS Visualization module

A drupal module for GWAS signals visualization in ZEAMAP.

The visualization mainly include two plots: Navigational Manhattan Plot and Detailed Scatter Plot

• Navigational Manhattan Plot

  This panel shows the most significant P-value (Y-axis) between the selected trait and the genetic variants within 500Kb sliding window of the genome (X-axis). You can navigate to your interested region by zoom and drag. Click on the region will generat a gray vertical indicator, and draw 'Detailed Scatter Plot' of this region below.

• Detailed Scatter Plot

  This panel shows the detailed plot of the variants and the genes within a certain region. Currently, only variants with -Log10(P-value) greater than 5 were displayed. The dots were colored by LD r2 value with the 'ref-variant' ( If not specified, the variant with the most significant P-value was set as the default ref-variant. ). The gene information tooltip provides interfaces for connecting with the gene detailed information, genome browser and eQTL signals. Please notice that the min and max plot regions of the scatter plot are 20 Kb and 1 Mb, respectively. If your input region was smaller than 20 Kb (or larger than 1Mb), the flanking 20 Kb (or 1 Mb) of the middle position was plotted.

Find a demo here: DEMO

Platform

• Drupal 7.x
• Tripal 7.x-3.x

Prerequisite

• csvtk (version 0.16.0 was used in ZEAMAP)
• locuszoom (version 0.9.1 was used in ZEAMAP)
• ztree (version 3 was used in ZEAMAP)
• echarts (version 4.2.1 was used in ZEAMAP)

Installation and Usage

1. Make sure all the prerequisite packages were correctly installed, and csvtk was added to the $PATH variable.

2. Download this repository, switch to drupal environment, and lunch this module with drush en -y zmap_gwasvis

3. Prepare necessary information and save to related tables in database as follows:

   Table_Name	Description
   zmap_gwasviz_assoc	stores significant P values and necessary information of each variant-trait association
   zmap_gwasviz_trait_category	stores trait category information
   zmap_gwasviz_[gene/exon/transcript]	stores gene annotations for locuszoom visualization

   The format of each table were listed as follows:

   zmap_gwasviz_assoc

   Trait	Variant	Chr	Position	-log(P-value)	Ref-allele	Alt-allele
   SA	chr1.s_29106	1	29106	5.79988374054394	A	G
   SA	chr1.s_34867	1	34867	5.12419680136797	A	T
   SA	chr1.s_111303	1	111303	5.87131754204541	T	C

   zmap_gwasviz_trait_category

   Column 1: number of lines
   Column 2: trait_id or Category_id
   Column 3: hierarchy orders
   

   No	Name	Category
   1	AminoAcid	0
   2	Ala	1
   3	Arg	1
   4	Asp	1
   5	Cys	1

   zmap_gwasviz_[gene/exon/transcript]

   ==> zmap_gwasviz_gene <==
   # GeneID GeneName Chr start end strand
   Zm00001d027230  Zm00001d027230  1       44289   49837   +
   Zm00001d027231  Zm00001d027231  1       50877   55716   -
   Zm00001d027232  Zm00001d027232  1       92299   95134   -
   
   ==> zmap_gwasviz_transcript <==
   #GeneID TranscriptID TranscriptID chr start end strand
   Zm00001d027230  Zm00001d027230_T001     Zm00001d027230_T001     1       44289   49837   +
   Zm00001d027231  Zm00001d027231_T001     Zm00001d027231_T001     1       50877   51964   -
   Zm00001d027231  Zm00001d027231_T002     Zm00001d027231_T002     1       50877   55716   -
   
   ==> zmap_gwasviz_exon <==
   #GeneID TranscriptID ExonID chr start end strand
   Zm00001d027230  Zm00001d027230_T001     Zm00001d027230_T001.exon1       1       44289   44947   +
   Zm00001d027230  Zm00001d027230_T001     Zm00001d027230_T001.exon2       1       45666   45803   +
   Zm00001d027230  Zm00001d027230_T001     Zm00001d027230_T001.exon3       1       45888   46133   +
   

4. Prepare a slide-window gwas -log(P-value) file that includes all traits with format:

   Chr	Region	Trait1	Trait2	Trait3	Trait4	Trait5
   chr1	1:0-500000	2.31630146832606	1.80738619280076	2.3600932652674	3.4697375322046	2.81576439173472
   chr1	1:500000-1000000	2.16586921946003	2.47204817043131	2.44478374829681	2.3009311614868	3.06381763398639
   chr1	1:1000000-1500000	2.20326973727822	2.14769705404575	2.80501221615503	2.62926990990414	3.24533370587843
   chr1	1:1500000-2000000	2.45927445908454	2.40150025060532	3.42899149389656	3.20341456675297	4.17005330405836
   chr1	1:2000000-2500000	2.77801464282688	2.4586176059459	2.7616131219865	3.05707419839616	3.24747447471538
   chr1	1:2500000-3000000	4.03574036980315	2.51863176692419	2.83982209620494	3.03474278058476	3.924796230317
   ...	...	...	...	...	...	...

   and put (or link) the file into Drupal public file directory sites/default/files/gwasviz_74_trait_win500K.tsv.

5. Prepare a directory that stores pairwise LD scores of variants for each trait, and the LD file should be named with trait name as prefix and ".LD" as suffix with format as follows (no header line):

   Site1	Site2	R2
   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

   and then put (or link) the directory to sites/default/files/zmap_gwasviz_74_trait_LD