[genoPlotR-help] genoplotR help with graphic presentation or CDS and names

[Lionel Guy]

Hi Diane, 

Nice plot! 
The option you’re looking for is gene_type. You can change it for example by doing:

geneA.seq$gene_type <- “arrow”

To see all gene types, look into the examples of gene_types. What you are looking for is probably “arrow” or “block”:

?gene_types

To label clusters, you need to use the “annotation” argument of plot_gene_map. To generate an annotation object, use annotation or the auto_annotate:

annotA <- auto_annotate(geneA.seq)

and so on for the other dna_segs and then 

plot_gene_map(dna_segs=*all my seg files* ), comparisons=*all my comparison files*), annotations=*all your annotations*, override_color_schemes=TRUE, global_color_scheme=c("e_value", "auto", "grey", "0”))

To generate a newick file, you need to obtain a tree, or you can write it yourself. This is a bit beyond the scope of the help list, but look into RAxML or other phylogeny programs. Definition of Newick format is here: http://evolution.genetics.washington.edu/phylip/newicktree.html. 

Hope that helps.

Cheers,

Lionel

> On 25 Jan 2017, at 19:18 , Artemis H <hatziiod at gmail.com> wrote:
> 
> Hello,
> 
> I've just tried to use genoplotR for the first time. I used read_dna_seg_from_genbank to import CDS info of cluster genes and read_comparison_from_blast to read  blastn comparison files. I checked them all with is.dna_seg and is.comparison and they all came out TRUE. Finally I used plot_gene_map(dna_segs=*all my seg files* ), comparisons=*all my comparison files*),override_color_schemes=TRUE, global_color_scheme=c("e_value", "auto", "grey", "0")). 
> 
> With this process I end up with a nice image which seems to show the blastn conserved regions but instead of CDS boxes I get thin blue dispersed lines along my stick cluster and I can't seem to find how to give each cluster a name. I've attached the usual output. 
> 
> I would like to ask first, how can I label the clusters, secondly how can I make the CDS show for each cluster as a box or arrow, thirdly how does one go about generating a newick2phylog file with the raw data?
> I'm pasting an example of a dna_seg object in case that helps:
> > geneA.seq
>    name start   end strand length pid gene synonym product  proteinid feature
> 1  geneA   828  1001      1     57  NA geneA      NA    geneA CD352.1     CDS
> 2  geneB  1109  4090      1    993  NA geneB      NA    geneB CD353.1     CDS
> 3  geneT  4101  5903      1    600  NA geneT      NA    geneT CD354.1     CDS
> 4  geneC  5896  7140      1    414  NA geneC      NA    geneC CD355.1     CDS
> 5  geneI  7137  7874      1    245  NA geneI      NA    geneI CD356.1     CDS
> 6  geneP  7876  9924      1    682  NA geneP      NA    geneP CD357.1     CDS
> 7  geneR  9993 10679      1    228  NA geneR      NA    geneR CD358.1     CDS
> 8  geneK 10672 12015      1    447  NA geneK      NA    geneK CD359.1     CDS
> 9  geneF 12114 12791      1    225  NA geneF      NA    geneF CD360.1     CDS
> 10 geneE 12793 13521      1    242  NA geneE      NA    geneE CD361.1     CDS
> 11 geneG 13508 14152      1    214  NA geneG      NA    geneG CD362.1     CDS
>    gene_type  col lty lwd pch cex
> 1       bars blue   1   1   8   1
> 2       bars blue   1   1   8   1
> 3       bars blue   1   1   8   1
> 4       bars blue   1   1   8   1
> 5       bars blue   1   1   8   1
> 6       bars blue   1   1   8   1
> 7       bars blue   1   1   8   1
> 8       bars blue   1   1   8   1
> 9       bars blue   1   1   8   1
> 10      bars blue   1   1   8   1
> 11      bars blue   1   1   8   1
> 
> 
> Thank you in advance, any help and tips would be appreciated.
> Diane
> 
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--
Lionel Guy
Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
phone: +46 18 471 4246; mobile +46 73 976 0618; postal address: Box 582, SE-751 23 Uppsala; visiting address: BMC D7:304c, Husargatan 3, SE-752 37 Uppsala
lionel.guy at imbim.uu.se