Introduction

The Manhattan chart can display the values of regions on multiple chromosomes. You can use the plotManhattan of the Sushi package.

Code explanation

Input

• bed format data frame

head(Sushi_GWAS.bed)

 Structure are as follows

 chr.hg18 pos.hg18 pos.hg18.1 rsid pval.GC.DBP V6
 chr1 1695996 1695996 rs6603811 0.003110 .
 chr1 1696020 1696020 rs7531583 0.000824 .
 chr1 1698661 1698661 rs12044597 0.001280 .
 chr1 1711339 1711339 rs2272908 0.001510 .
 chr1 1712792 1712792 rs3737628 0.001490 .
 chr1 1736016 1736016 rs12408690 0.004000 
 chr11 2286805 2286832 GGTGAGGGCCAGCAGCTCCCTGGGGGG 250 1

• Genome length data frame

  head(Sushi_hg18_genome)

 The structure is as follows

    V1 V2
 chr1 247249719
 chr10 135374737
 chr11 134452384
 chr12 132349534
 chr13 114142980
 chr14 106368585

Code example

library('Sushi')  # Load Sushi package

Sushi_data = data(package ='Sushi') # List Sushi ownn data
data(list = Sushi_data$results[,3]) # Load ata

plotManhattan(bedfile=Sushi_GWAS.bed,pvalues=Sushi_GWAS.bed[,5],
col=SushiColors(6),genome=Sushi_hg18_genome,cex=0.75)

labelgenome(genome=Sushi_hg18_genome,n=4,scale="Mb",
edgeblankfraction=0.20,cex.axis=.5)  #Add genome coordinate position

axis(side=2,las=2,tcl=.2)  # Add a coordinate axis, here is the y axis

mtext("log10(P)",side=2,line=1.75,cex=1,font=2) # add tag
mtext("chromosome",side=1,line=1.75,cex=1,font=2)

Reference

https://www.bioconductor.org/packages/release/bioc/vignettes/Sushi/inst/doc/Sushi.pdf