In YTLogos/ttplot: Tao Yan's Plot Toolkit

knitr::opts_chunk$set(
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Overview

This package is just developed to finish my project. So most of scripts are NOT stable enough. By wrapping some functions from other useful packages, it's easy for us to finish our jobs.

Installation

This packages dependent on some other packages:vcfR,dplyr,genetics,LDheatmap, ...

The dependent packages will be installed at the time you install the package ttplot

#install the ttplot package from Github
devtools::install_github("YTLogos/ttplot")

Usage

Until now there are just several functions

Draw the LDheatmap from the VCF format file (plink format)

VCF (Variant Call Format) is a text file format. It contains meta-information lines, a header line, and then data lines each containing information about a position in the genome. There is an example how to draw LDheatmap from data in VCF file(plink format). The VCF file looks like:

#This is a test vcf file (test.vcf) 

##fileformat=VCFv4.3
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS      ID         REF   ALT    QUAL  FILTER   INFO                             FORMAT       NA00001         NA00002          NA00003
20     14370    rs6054257  G     A      29    PASS    NS=3;DP=14;AF=0.5;DB;H2           GT:GQ:DP:HQ  0|0:48:1:51,51  1|0:48:8:51,51   1/1:43:5:.,.
20     17330    .          T     A      3     q10     NS=3;DP=11;AF=0.017               GT:GQ:DP:HQ  0|0:49:3:58,50  0|1:3:5:65,3     0/0:41:3
20     1110696  rs6040355  A     G,T    67    PASS    NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ  1|2:21:6:23,27  2|1:2:0:18,2     2/2:35:4
20     1230237  .          T     .      47    PASS    NS=3;DP=13;AA=T                   GT:GQ:DP:HQ  0|0:54:7:56,60  0|0:48:4:51,51   0/0:61:2
20     1234567  microsat1  GTC   G,GTCT 50    PASS    NS=3;DP=9;AA=G                    GT:GQ:DP     0/1:35:4        0/2:17:2         1/1:40:3

This kind of VCF is very large, so first we can use plink to recode the VCF file

$ plink --vcf test.vcf --recode vcf-iid --out Test -allow-extra-chr

So the final VCF file we will use is looks like：

##fileformat=VCFv4.2
##fileDate=20180905
##source=PLINKv1.90
##contig=<ID=chrC07,length=31087537>
##INFO=<ID=PR,Number=0,Type=Flag,Description="Provisional reference allele, may not be based on real reference genome">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  R4157   R4158
chrC07  31076164    .   T   G   .   .   PR  GT  0/0 0/1
chrC07  31076273    .   G   A   .   .   PR  GT  0/0 0/1
chrC07  31076306    .   G   T   .   .   PR  GT  0/0 0/0

In the extdata directory there is one test file: test.vcf. We can test the function:

library(ttplot)
test <- system.file("extdata", "test.vcf", package = "ttplot")
ttplot::MyLDheatMap(vcffile = test, title = "My gene region")

SessionInfo

sessioninfo::session_info()

YTLogos/ttplot documentation built on Aug. 20, 2019, 8:18 p.m.