Question: How to add significant cut off in manhattan plot
0
gravatar for Manoj
4 months ago by
Manoj30
Canada
Manoj30 wrote:

Hi, I need to add significant cut off value (<0.01) in my circular manhattan plot. Please see following code that I am using for plotting and link of plot.

CMplot(manhat,plot.type="c",r=0.6, col=c("grey30","grey60"),chr.labels=c("Chr1", "Chr2",  "Chr3", "Chr4", 
"Chr5","Chr6","Chr7","Chr8","9","Chr10","Chr11","12","Chr13","Chr14"),

 LOG10=TRUE, cir.chr.h=0.5,amplify=TRUE,threshold.lty=c(1,2),threshold.col=c("red",
"blue"),

 signal.line=1,signal.col=c("red","green"),chr.den.col=c("darkgreen","yellow","red"),
 outward=FALSE,file="jpg",dpi=600,file.output=TRUE,verbose=TRUE,width=10,height=10)

enter image description here

R • 227 views
ADD COMMENTlink modified 4 months ago by ATpoint28k • written 4 months ago by Manoj30
1

How exactly do you envision it to be added? Just as a number printed on the plot? Or via a line/asterisk/....?

ADD REPLYlink written 4 months ago by Friederike5.2k

Can you please elaborate your answer, I am not certain to understand?

ADD REPLYlink written 4 months ago by Manoj30

What is your expected plot look like?

(please format your code, use some spaces, newlines.)

ADD REPLYlink modified 4 months ago • written 4 months ago by zx87548.8k

Here, is a example excel file for manhattan plot, that I need to put significant cut off values at each bar on circular manhattan plot.

SNP CHR BP  P   
 bio137 1   1077947 1.00E-05     
 bio237 1   849080  5.08E-05  
 bio337 1   387297  9.48E-04  
 bio437 1   643714  9.48E-04  
 bio537 1   1300841 1.17E-03  
 bio637 1   1307435 1.77E-03  
 bio737 1   68905   2.65E-03
ADD REPLYlink modified 4 months ago by RamRS25k • written 4 months ago by Manoj30

It is still unclear what you want. Please try, and be it by hand in Powerpoint, to make a representative picture so people understand what you would like to do.

ADD REPLYlink written 4 months ago by ATpoint28k

Hi, I need to add p<0.01 cut off for this plot.

ADD REPLYlink written 4 months ago by Manoj30
1

Please do not delete posts that have received comments.

ADD REPLYlink written 4 months ago by genomax76k

Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)

ADD REPLYlink written 4 months ago by RamRS25k
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