To plot values of LOD score a long of genome

[Rodrigo Lima]

Hi, all

I have a data frame from a QTL analysis in plant with four columns: Markers, Chromosome, Genetic Map (in centimorgan) and o LOD score values. I would like to plot this value in a graph like the graph attached.  

marker	chr	gen_map	LOD
rs1	1	0	14.740
rs1	1	0.9	14.350
rs3	1	3.7	11.806

Are there someone that can help me, please?

Thank you so much.

Rodrigo

 

[Benilton Carvalho]

The plot didn't come through (but it's often good practice not attach files to messages sent to a mailing list)... Looks like you want to take a look at the ggbio package (BioConductor)

http://www.bioconductor.org/packages/2.12/bioc/vignettes/ggbio/inst/doc/ggbio.pdf

Look for Manhattan Plot...

If you rather do that manually, assuming that your data.frame is sorted, you may want to do something along the lines of:

ggplot(dat, aes(cumsum(gen_map), LOD, colour=chr) + geom_point()

b

2013/7/16 Rodrigo Lima <rodrigo...@gmail.com>

 

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[Rodrigo Lima]

Hi, Benilton

Thank you so much for your help. I am going to try to do it.

Rodrigo.

Rodrigo Oliveira de Lima

PhD Student in genetics and breeding

Department of General Biology

Federal University of Viçosa, Brazil

Department of Agronomy

University of Wisconsin-Madison, USA

Phone:(608)698-6116

CV: http://lattes.cnpq.br/2761299616351806