[genoPlotR-help] scale_cex parameter

[Michael Muratet]

On Oct 4, 2012, at 11:44 AM, Lionel Guy wrote:

> Hi Mike,
>
> On 4 Oct 2012, at 18:20 , Michael Muratet wrote:
>
>> Is the scale_cex parameter supposed to control the dna_seg_scale  
>> that appears below the dna_seg or the little 'legend' scale that  
>> appears to the right? I see no effect on either scale.
>
> The scale_cex controls the size of the labels of the dna_seg_scale  
> (not the little legend). To convince yourself, try:
>
> library(genoPlotR)
> data(three_genes)
> plot_gene_map(dna_segs, comparisons, dna_seg_scale=TRUE, scale_cex=2)
Is there a way to make the little legend smaller? The plot looks a  
little too busy with the full dna_seg_scale.
>
>> Is there a way to make the arrow head size fixed?
>
> There is a way to fix the arrow head size, using arrow_head_len  
> parameter
> plot_gene_map(dna_segs, comparisons, arrow_head_len=10)
>
>
>> I'm plotting nested repeats in a viewport after the example in the  
>> vignette. I'd like the arrows in each viewport to be proportional  
>> to the true length (otherwise all the arrows extend from margin to  
>> margin). I don't see a way to do this from within genoplotr and I'm  
>> a newbie when it comes to grid plotting. Can anyone offer a  
>> suggestion for an approach?
>
> I'm not sure I understand what you really want to do... Why do your  
> arrows extend to margin from margin? Maybe you need to load features  
> that correspond to your repeats... what is the "true length"?

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.

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?

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
>>
>>
>>
>>
>>
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>
>
>
>
>
>
>
>
>

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