Tutorial for Circular and

Rectangular Manhattan

Plots

Avjinder Singh Kaler

This tutorial is used to graph Manhattan plots in

Circular and Rectangular forms using R package

CMplot. You have any question, you can contact me on

this email askaler@uark.edu .

Download and Install software. 1. R program https://cran.r-project.org/bin/windows/base/ 2. R Studio

https://www.rstudio.com/products/rstudio/do

wnload/

Steps in Manhattan Plots

Step 1: File Formatting

You can use any GWAS results output file. Your

first Column should be “SNP”, second column be

“chromosome”, third column be “Position”,

“fourth and remaining columns” you should p-

values of Trait. You can use Trait name in

column.

Save file as “.csv”.

Here is the example of file.

Step 2: Install and Load the CMplot package

install.packages("CMplot")

library(“CMplot”)

Step 3: Set working directory and import data

#Set your working directory where you have your

data files.

Step 4: Read your “.csv” file

Y <- read.csv("filename.csv”)

attach(Y)

CMplot (cc1, plot.type="b",threshold=c(10),

threshold.col=c('red'),multracks=TRUE,cir.legen

d=TRUE,signal.col=NULL,signal.cex=2,outward

=TRUE,r=12,cex.axis=1.5,cir.chr.h=2,cir.chr.col=

NULL,cir.legend.cex=0.5,threshold.lwd=1,H=6,ci

r.band=15,box=TRUE)

#Different graphs; circular, rectangular, and QQ

plots will be saved in your directory.

#Note: If you want to change above parameters,

you can visit here ftp://cran.r-project.org/pub/R/web/packages/CMplot/CMplot.pdf

and read Arguments section.

For other Tutorials, you can visit here: http://www.slideshare.net/AvjinderSingh