tutorial for circular and rectangular manhattan plots
TRANSCRIPT
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Tutorial for Circular and
Rectangular Manhattan
Plots
Avjinder Singh Kaler
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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 [email protected] .
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/
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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”)
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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.
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For other Tutorials, you can visit here: http://www.slideshare.net/AvjinderSingh