[genoPlotR-help] scale_cex parameter

[Lionel Guy]

Hi Mike, 
On 4 Oct 2012, at 21:19 , Michael Muratet wrote:

> Is there a way to make the little legend smaller? The plot looks a little too busy with the full dna_seg_scale.

Unfortunately not, but you can remove it (scale=FALSE)

> I have two features, one repeat nested in another. The containing repeats are all of the same family, but the length of their alignment varies on the chromosomes from one locus to the next. I am trying to capture that information in the length of the arrow so that if repeat_N is 1000 bp long and appears full length on chr_A but only 500 bp on chr_B that chr_B arrow is 50% of the chr_A arrow. The nested repeat then appears wherever it falls on the containing arrow. Also, because all the arrows have the same physical length but different logical lengths, the arrow heads appear differently.

I think other types of features might be your solution. I'd try side_blocks for a start (see further mail).

> If I plotted all the dna_segs in the same list and used limit_to_longest_dna_seg could I get the effect I want?

I don't think so... limit_to_longest_dna_seg only works when you have several dna_segs and comparisons: it directs how the dna_segs are placed with respect to each other (minimizing the size of the comparisons). Here you don't have comparisons...

Best,

Lionel

> Thanks for the help.
> 
> Mike
> 
>> 
>> If you want to personalize the shapes of the features, have a look at gene_types:
>> 
>> ?gene_types
>> example(gene_types)
>> 
>> HTH,
>> 
>> Lionel
>> 
>> 
>>> Cheers
>>> 
>>> Mike
>>> 
>>> Michael Muratet, Ph.D.
>>> Senior Scientist
>>> HudsonAlpha Institute for Biotechnology
>>> mmuratet at hudsonalpha.org
>>> (256) 327-0473 (p)
>>> (256) 327-0966 (f)
>>> 
>>> Room 4005
>>> 601 Genome Way
>>> Huntsville, Alabama 35806
>>> 
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> genoPlotR-help mailing list
>>> genoPlotR-help at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genoplotr-help
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
> 
> Michael Muratet, Ph.D.
> Senior Scientist
> HudsonAlpha Institute for Biotechnology
> mmuratet at hudsonalpha.org
> (256) 327-0473 (p)
> (256) 327-0966 (f)
> 
> Room 4005
> 601 Genome Way
> Huntsville, Alabama 35806
> 
> 
> 
> 
> 

--
Lionel Guy 
Molecular Evolution, Uppsala University, Uppsala, Sweden
postal address: Box 596, SE-751 24 Uppsala; visiting address: BMC C6:305d, Husargatan 3, SE-752 37 Uppsala
phone: +46 18 471 6129, mobile +46 73 976 0618
lionel.guy at icm.uu.se