Comments (3)
It sounds quite strange, did you try to update the package to the latest version?
from cmplot.
Thanks for replying.
My version of CMplot is 4.5.1.
1)
I think it's related with some parameters I do not know. So I have to keep it as amplify=TRUE, which is as default. When I add only "amplify=FALSE", I got the Error.
> CMplot(my_data,type="p",plot.type="m",LOG10=TRUE,amplify=FALSE,
+ col = "grey45", ylim=c(3,45),
Error: unexpected input in:
"CMplot(my_data,type="p",plot.type="m",LOG10=TRUE,amplify=FALSE,
col = "grey45", ylim=c(3,45), "
My Work Code is like
CMplot(my_data,type="p",plot.type="m",LOG10=TRUE,
col = "grey45", ylim=c(3,45),
cex=0.5, lab.cex=1.2, ylab.pos=1.8,
pch=19,
signal.col="red",
signal.pch=pchs[m],
signal.cex=0.5,
threshold=1e-20,
threshold.lty=3,threshold.lwd=c(1,1),
main=m_names[m],
file.output=F,
verbose=TRUE,width=8,height=5,
points.alpha=255,legend.ncol=3, legend.pos="left")
2)
And Another question is about circle plot. I do not know why my plot have some grey box (looks like the SNPs density) at every circle.
My Work Code is like
CMplot(data, plot.type="c", r=3, multraits=TRUE,outward=FALSE,
cex = 0.2,
col="green"
chr.border=FALSE,
cir.chr.h = 2, chr.den.col="grey60",
chr.labels=paste("Chr",c(1:20),sep=""),
cir.axis.grid=FALSE,
cir.axis=FALSE,
signal.cex = 0.2,
signal.col="black",
threshold=0.01/nrow(data), threshold.lty=3,threshold.lwd=c(1,1),
file="pdf",file.name=filen,
file.output=TRUE,verbose=TRUE,width=10,height=10,
points.alpha=100,legend.ncol=6, legend.pos="left")
Thans~
from cmplot.
Thank you for the detailed feedback.
Question 1. I have tried the similar script to run CMplot using the tutorial data, it works fine. I guess there may be some unqualified or unexpected symbols in your script. Or if it's really hard to locate the problem, you can try to reproduce the same error using tutorial data, and then send me the running script for debugging.
Question 2. That is because CMplot will drew a line across circles at the position where there is a significant SNP for at least one trait, you can turn off these lines by setting the argument "signal.line=NULL".
from cmplot.
Related Issues (20)
- p values should be at range of (0, 1). HOT 6
- how to highlight snp in outlined circle
- how to alter multiple track qq plots HOT 1
- bin.size doesn't look right HOT 3
- Error in Pmap[, 1] : incorrect number of dimensions HOT 2
- Adding tags to significant points in multitrait / multitrack QQ plots HOT 2
- p values should be at range of (0, 1). HOT 6
- how to get rid of grey shadows when applying threshold HOT 2
- Chromosome order in marker density plot HOT 1
- I have only one-layer of circle plot HOT 1
- Multi-traits of Manhattan cannot change the chromosomal color and add some SNPS to the tag
- Error in plot.new() HOT 1
- Error in p values should be at range of (0, 1). HOT 3
- Density Plot x-axis ticks HOT 1
- Is it possible to save the file as a vector image? HOT 1
- Can CMplot break the Yaxis? HOT 1
- Rectangular manhattan plot - color the signal with 2 different significance lines HOT 2
- hightlight is not working for multi-traits rectangle manhattan plot HOT 2
- chr labels order problem HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from cmplot.