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-logten p is a good default to plot, but with other types of genome wide data to plot and look at peaks for, it'd be great to have an argument to just straight plot the data provided in p, (and probab…
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Hello,
I have gwas results from PLINK or in similar formats (with CHR, SNP, BP, and P columns). I've been using qqman to obtain qqplots and manhattan plots and I'm really pleased with this tool.
Mor…
isp2 updated
10 years ago
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Mike's idea... test it out.
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Dan, can you help look at a problem reported in this [blog comment](http://gettinggeneticsdone.blogspot.com/2011/04/annotated-manhattan-plots-and-qq-plots.html?showComment=1381753982225#c6822147450013…
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working on [code-from-blog-post.r](https://github.com/stephenturner/qqman/blob/master/code-from-blog-post.r), getting error at line 19: `D'oh! Highlight vector/list must be a subset of the SNP column.…
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Thank you for your great code.
I found a typo in qqman.r line 134 (in the gg.manhattan function)
"plot=plot+scale_colour_manual(value=mycols)"
seems to be a typo of
"plot=plot+scale_colour_manual(val…
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with ability to plot entire genome staggered e.g:
https://github.com/brentp/bio-playground/tree/master/plots
or one chromosome at a time. Or all chromosomes stacked. e.g.
[chr1]
[chr2]
...
[chrY]
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I just noticed that the documentation for the `Pipeline` class doesn't properly show up in the [generated HTML](http://scikit-learn.org/dev/modules/generated/sklearn.pipeline.Pipeline.html). I tried t…
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This was reported by Aleksey G:
```
I tried to install package "cluster" for R and got this:
----------------------------------------------------------------------
| Sage Version 4.0.2, Release Da…