Question: How to add significant cut off in manhattan plot
0
gravatar for Manoj
5 weeks 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 • 173 views
ADD COMMENTlink modified 4 weeks ago by ATpoint24k • written 5 weeks 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 5 weeks ago by Friederike5.2k

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

ADD REPLYlink written 5 weeks ago by Manoj30

What is your expected plot look like?

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

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by zx87548.3k

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 5 weeks ago by RamRS24k • written 5 weeks 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 weeks ago by ATpoint24k

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

ADD REPLYlink written 4 weeks ago by Manoj30
1

Please do not delete posts that have received comments.

ADD REPLYlink written 4 weeks ago by genomax73k

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 5 weeks ago by RamRS24k
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