[genoPlotR-help] scale_cex parameter

[Lionel Guy]

It seems it works for me... You may have an issue with transparency colors.

What if you try to change the gene_type for both dna_segs (and colors as well):

temp[[1]]$gene_type <- "side_blocks"
temp[[2]]$gene_type <- "side_blocks"
temp[[1]]$col <- c("red", "blue")
temp[[2]]$col <- c("red", "blue")
plot_gene_map(temp)

Then you can fiddle with your own gene_types, as I was indicating in my first email.

Cheers,

Lionel

On 4 Oct 2012, at 21:31 , Michael Muratet wrote:

> Hello again
> 
> The multiple dna_segs apparently won't work for me:
> 
> > temp
> [[1]]
>  name   start     end strand       col lty lwd pch cex gene_type
> 1 LG_1 1138831 1138900     -1 #00FF00FF   1   1   8   1    arrows
> 2 LG_1 1138141 1142749      1 #44444411   1   1   8   1    arrows
> 
> [[2]]
>  name   start     end strand       col lty lwd pch cex gene_type
> 1 LG_1 9241059 9241128      1 #00FF00FF   1   1   8   1    arrows
> 2 LG_1 9240763 9242602     -1 #44444411   1   1   8   1    arrows
> 
> > is(temp[[1]])
> [1] "dna_seg"
> > is(temp[[2]])
> [1] "dna_seg"
> > plot_gene_map(dna_segs=temp)
> 
> This produces a single arrow. I presume it's because it's widely separated loci on the same scaffold.
> 
> I am trying to create something a little more informative and intuitive than a text table. It's almost there but I'm trying to tweak the last few bits.
> 
> 
> 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
> 
> 
> 
> 
> 

--
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