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

Mon Feb 2 23:53:53 CET 2015

Lionel,

I've discussed the HPV16 graphic from your package with a senior genomics person here. She recognized that it was useful to be able to read Genbank PaVE files directly. I've passed on the script that I was using, which uses your code to get coloured genes.

Thanks for your help. We will look more at the package as time permits.

Gordon

On 2015-02-02, at 11:41 AM, Lionel Guy wrote:

Hi Gordon,

My complete code is:

library(genoPlotR)
hpv.df <- read_dna_seg_from_file("/Users/lguy/Desktop/tmp/HPV16.ref.PaVE.gbk", tagsToParse=c("CDS"), fileType = "detect", meta_lines = 2, gene_type = "blocks", header = TRUE, extra_fields = c("db_xref", "transl_table"))
hpv.df$col <- rainbow(nrow(hpv.df))
hpv.df$gene_type <- "arrows"
annot <- annotation(x1=middle(hpv.df), text=hpv.df$name, rot=0)
plot_gene_map(list(hpv.df), annotations=annot)

And it yields the following plot:

<PastedGraphic-1.png>

HTH,

Lionel
On 2 Feb 2015, at 17:58 , Gordon Robertson <grobertson at bcgsc.ca<mailto:grobertson at bcgsc.ca>> wrote:

Thank you. Your code generated a graphic with a single line of dark blue arrows (for genes), with gene symbols above the arrows. I've looked briefly at the vignette and the help page for gene_types, but I do not have time right now to work with this information.

Gordon

On 2015-02-01, at 11:48 PM, Lionel Guy wrote:

Hi Gordon,

I haven't worked extensively with eukaryotic sequences, so in some ways the gbk parser might be behaving strangely with spliced sequences, for example.
That being said, there are more blocks, they are just all the same color. Try

hpv.df$col <- rainbow(nrow(hdv.df))
hpv.df$gene_type <- "arrows"
annot <- annotation(x1=middle(hpv.df), text=hpv.df$name, rot=0)
plot_gene_map(list(hpv.df), annotations=annot)

that should help you see better.

To plot different genes on different lines, you'll either have to separate them on different dna_segs, or write your own plotting functions. See the vignette for genoPlotR or the help page for function gene_types

Kind regards,

Lionel

On 2 Feb 2015, at 0:04 , Gordon Robertson <grobertson at bcgsc.ca<mailto:grobertson at bcgsc.ca>> wrote:

Thanks Lionel

That worked. It gave me a two-block graphic (attached). What I'd like is something like the CDS (gene) view (attached). How would I get that?

Thanks,

Gordon
--
Gordon Robertson
Canada's Michael Smith Genome Sciences Centre
BC Cancer Agency
Vancouver BC Canada
www.bcgsc.ca<http://www.bcgsc.ca/>
T: 604-707-5900 x675416
Skype: a.gordon.robertson

On 2015-02-01, at 1:38 PM, Lionel Guy wrote:

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<mailto: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<mailto: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<mailto:lionel.guy at imbim.uu.se>

<screenshot_585.tif><PastedGraphic-1.pdf>

--
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<mailto:lionel.guy at imbim.uu.se>

--
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<mailto:lionel.guy at imbim.uu.se>

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