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

[Artemis H]

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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