[genoPlotR-help] genoPlotR question: visualizing an HPV reference genome

[Lionel Guy]

Hi Gordon,

Thanks for your interest in genoPlotR.

The dna_segs argument of plot_gene_map should be a list of dna_seg objects. To plot one single dna_seg, use a list composed of a single dna_seg object:

plot_gene_map(list(hpv.df))

That should do the trick.
HTH,

Lionel


> On 1 Feb 2015, at 21:17 , Gordon Robertson <agrobertson at telus.net> wrote:
> 
> Hi Lionel,
> 
> I'm exploring (assessing) the genoPlotR package as a simple and extensible way of drawing information on viral integration into human genes in cancer. There are a number of components to this. I'm trying to take a first step. 
> 
> I'm also looking at the Gviz package. 
> 
> As a first step I've downloaded an HPV16 reference genome Genbank-format file from PaVE (attached). The file loads easily into genoPlotR. Now I'd like to plot the genes in the genome. 
> 
> library(genoPlotR)
> 
> # HPV16 reference genome
> hpv.df <- read_dna_seg_from_file("/Users/grobertson/resources/genomic_data/viral/PaVE/HPV16.ref.PaVE.GenBank.format.txt", tagsToParse=c("CDS","misc_feature","gene"), fileType = "detect", meta_lines = 2, gene_type = "blocks", header = TRUE, extra_fields = c("db_xref", "transl_table"))
> 
> str(hpv.df)
> # Classes ‘dna_seg’ and 'data.frame':  25 obs. of  19 variables:
> #$ name        : chr  "E1" "E2" "E4" "E5_ALPHA" ...
> #$ start       : num  865 2756 3333 3850 83 ...
> #...
> 
> plot_gene_map(hpv.df)
> Error in plot_gene_map(hpv.df) : 
>   Argument dna_segs must be a list of dna_seg objects
> 
> Would you be willing to help me resolve this? I apologize for emailing so early in assessing your package, but I have very limited time for resolving this visualization issue. I'm using R 3.1.2 on OS X, and working in the latest RStudio. 
> 
> Thank you. 
> 
> Gordon
> --
> Gordon Robertson
> agrobertson at telus.net
> 
> 
> 
> <HPV16.ref.PaVE.GenBank.format.txt>

--
Lionel Guy
Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
postal address: Box 582, SE-751 23 Uppsala; visiting address: BMC D7:3, Husargatan 3, SE-752 37 Uppsala
phone: +46 73 976 0618
lionel.guy at imbim.uu.se