[genoPlotR-help] scale_cex parameter

[Lionel Guy]

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 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"?

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
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