[genoPlotR-help] genoPlotR-help Digest, Vol 13, Issue 1

Fri Sep 13 10:46:25 CEST 2013

Dear Dr. Lionel,
I have figured out the way and had generated the diagram. Thanks. 

Best regards,wing sze
From: howingsze86 at hotmail.com
To: genoplotr-help at lists.r-forge.r-project.org
Subject: RE: genoPlotR-help Digest, Vol 13, Issue 1
Date: Fri, 13 Sep 2013 08:33:18 +0800

Dear Dr. Lionel,
The questions that I'm going to ask might be too simple as I'm a newbie to R.
would like to ask how am I going to check where R was started?  (Provided that the Genbank 
les and their comparison have been saved underthe correct names in the directory where R was started). I'm using linux. 
I did not load the library(genoPlotR) at the first place. this is what I get after loading the library.
> sessionInfo()R version 2.14.1 (2011-12-22)Platform: i686-pc-linux-gnu (32-bit)
locale: [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    [7] LC_PAPER=C                 LC_NAME=C                  [9] LC_ADDRESS=C               LC_TELEPHONE=C            [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
attached base packages:[1] stats     graphics  grDevices utils     datasets  methods   base     > library(genoPlotR)Loading required package: gridLoading required package: ade4
Attaching package: ‘ade4’
The following object(s) are masked from ‘package:base’:
    within
> BH <- try(read_dna_seg_from_file("NC_005956.gbk"))Error in file(con, "r") : cannot open the connectionIn addition: Warning message:In file(con, "r") :  cannot open file 'NC_005956.gbk': No such file or directory

Sorry for asking such simple questions. please advice.
best regards,wing sze

> From: genoplotr-help-request at lists.r-forge.r-project.org
> Subject: genoPlotR-help Digest, Vol 13, Issue 1
> To: genoplotr-help at lists.r-forge.r-project.org
> Date: Thu, 12 Sep 2013 12:00:08 +0200
> 
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>    1. Re: could not find function	\"read_comparison_from_file
>       (Lionel Guy)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 12 Sep 2013 10:03:56 +0200
> From: Lionel Guy <guy.lionel at gmail.com>
> To: wing sze ho <howingsze86 at hotmail.com>
> Cc: Help for genoPlotR <genoplotr-help at lists.r-forge.r-project.org>
> Subject: Re: [genoPlotR-help] could not find function
> 	\"read_comparison_from_file
> Message-ID: <DF4C949A-48B6-44A1-858A-407392DF7DE8 at gmail.com>
> Content-Type: text/plain; charset=iso-8859-1
> 
> Hi Wing,
> 
> Have you loaded the library? 
> 
> > library(genoPlotR)
> 
> Can you mail the result of
> 
> > sessionInfo()
> 
> so that I can see which version of genoPlotR you are using?
> It's strange that it can perform the two first commands but breaks on the third one...
> 
> Cheers,
> 
> Lionel
> 
> On 12 Sep 2013, at 9:51 , wing sze ho <howingsze86 at hotmail.com> wrote:
> 
> > Dear Dr. Lionel,
> > 
> > Was trying to work on the examples in section 7.2.3 (Getting started with genoPlotR) and encountered some problem.
> > 
> > Below are the commands that i followed exactly according to the manual. However, it seems that "read_comparison_from_blast" couldn't be found. Please advice.
> > 
> > 
> > Loading Tcl/Tk interface ... done
> > Loading required package: stats
> > Loading required package: graphics
> > Loading required package: MASS
> > Loading required package: nnet
> > Loading required package: survival
> > Loading required package: splines
> > > BH <- try(read_dna_seg_from_file("NC_005956.gbk"))
> > > BQ <- try(read_dna_seg_from_file("NC_005955.gbk"))
> > > BH_vs_BQ <- try(read_comparison_from_blast("NC_005956_vs_NC_005955.blast"))
> > > xlims <- list(c(1,50000), c(1,50000))
> > > plot_gene_map(dna_segs=list(BH, BQ),
> > + comparisons=list(BH_vs_BQ),
> > + xlims=xlims,
> > + main="BH vs BQ, comparison of the first 50 kb",
> > + gene_type="side_blocks",
> > + dna_seg_scale=TRUE, scale=FALSE)
> > > BH_vs_BQ
> > [1] "Error in try(read_comparison_from_blast(\"NC_005956_vs_NC_005955.blast\")) : \n  could not find function \"read_comparison_from_blast\"\n"
> > attr(,"class")
> > [1] "try-error"
> > attr(,"condition")
> > <simpleError in doTryCatch(return(expr), name, parentenv, handler): could not find function "read_comparison_from_blast">
> > 
> > 
> > many thanks.
> > 
> > best wishes,
> > wing sze
> > 
> 
> --
> Lionel Guy
> Petterslundsgatan 24B, SE-75328 Uppsala
> email: guy.lionel at gmail.com, mobile: +46 (0)73 9760618, phone: +46 (0)18 410 7398
> 
> 
> 
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> End of genoPlotR-help Digest, Vol 13, Issue 1
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