<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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.<div><br></div><div>Gordon<br><div apple-content-edited="true">
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<br><div><div>On 2015-02-01, at 11:48 PM, Lionel Guy wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Gordon,<br><br>I haven't worked extensively with eukaryotic sequences, so in some ways the gbk parser might be behaving strangely with spliced sequences, for example. <br>That being said, there are more blocks, they are just all the same color. Try<br><br>hpv.df$col <- rainbow(nrow(hdv.df))<br>hpv.df$gene_type <- "arrows"<br>annot <- annotation(x1=middle(hpv.df), text=hpv.df$name, rot=0)<br>plot_gene_map(list(hpv.df), annotations=annot)<br><br>that should help you see better. <br><br>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<br><br>Kind regards,<br><br>Lionel<br><br><br><blockquote type="cite">On 2 Feb 2015, at 0:04 , Gordon Robertson <<a href="mailto:grobertson@bcgsc.ca">grobertson@bcgsc.ca</a>> wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks Lionel<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">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? <br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Gordon<br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">Gordon Robertson<br></blockquote><blockquote type="cite">Canada's Michael Smith Genome Sciences Centre<br></blockquote><blockquote type="cite">BC Cancer Agency <br></blockquote><blockquote type="cite">Vancouver BC Canada<br></blockquote><blockquote type="cite"><a href="http://www.bcgsc.ca">www.bcgsc.ca</a><br></blockquote><blockquote type="cite">T: 604-707-5900 x675416<br></blockquote><blockquote type="cite">Skype: a.gordon.robertson<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On 2015-02-01, at 1:38 PM, Lionel Guy wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Hi Gordon,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks for your interest in genoPlotR.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">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:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">plot_gene_map(list(hpv.df))<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">That should do the trick.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">HTH,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Lionel<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">On 1 Feb 2015, at 21:17 , Gordon Robertson <<a href="mailto:agrobertson@telus.net">agrobertson@telus.net</a>> wrote:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi Lionel,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">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. <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I'm also looking at the Gviz package. <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">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. <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">library(genoPlotR)<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"># HPV16 reference genome<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">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"))<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">str(hpv.df)<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"># Classes ‘dna_seg’ and 'data.frame': 25 obs. of 19 variables:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">#$ name : chr "E1" "E2" "E4" "E5_ALPHA" ...<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">#$ start : num 865 2756 3333 3850 83 ...<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">#...<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">plot_gene_map(hpv.df)<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Error in plot_gene_map(hpv.df) : <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> Argument dna_segs must be a list of dna_seg objects<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">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. <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Thank you. <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Gordon<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">--<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Gordon Robertson<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="mailto:agrobertson@telus.net">agrobertson@telus.net</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><HPV16.ref.PaVE.GenBank.format.txt><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">--<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Lionel Guy<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">postal address: Box 582, SE-751 23 Uppsala; visiting address: BMC D7:3, Husargatan 3, SE-752 37 Uppsala<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">phone: +46 73 976 0618<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="mailto:lionel.guy@imbim.uu.se">lionel.guy@imbim.uu.se</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><screenshot_585.tif><PastedGraphic-1.pdf><br></blockquote><br>--<br>Lionel Guy<br>Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden<br>postal address: Box 582, SE-751 23 Uppsala; visiting address: BMC D7:3, Husargatan 3, SE-752 37 Uppsala<br>phone: +46 73 976 0618<br><a href="mailto:lionel.guy@imbim.uu.se">lionel.guy@imbim.uu.se</a><br><br></div></blockquote></div><br></div></body></html>