From guy.lionel at gmail.com  Mon Apr 13 17:20:18 2015
From: guy.lionel at gmail.com (Lionel Guy)
Date: Mon, 13 Apr 2015 17:20:18 +0200
Subject: [genoPlotR-help] Question about plot
In-Reply-To: <20150413150729.8B0FD18794D@r-forge.r-project.org>
References: <20150413150729.8B0FD18794D@r-forge.r-project.org>
Message-ID: <F314A362-6007-4C8A-9FB7-6B8389B63636@gmail.com>

Hi Bo Zhu,

Could you please give me the exact commands you input and the output of the program? 
plot_gene_map() doesn't "print" anything, but opens a new window or outputs to the latest graphical device if any is open...

Cheers,

Lionel

> On 13 Apr 2015, at 17:07 , Bo Zhu <bozhu at ims.u-tokyo.ac.jp> wrote:
> 
> Hey Guys,
>    I have one question about this software. I just start to learn this software and find it is pretty awesome. One problem, I don't need comparison function, gene structure and strand is enough for me. In this case, I tried to type the example 7.1.1 to learn. After the dna_segs <- list(dna_seg1, dna_seg2, dna_seg3) and I direct to print out by using 
> plot_gene_map(dna_segs = dna_segs). But I found nothing print out. Could you please tell me what's wrong here and please let me know how to solve this problem. Thanks
> 
> Best
> Bo Zhu

--
Lionel Guy 
F?lhagsleden 13, SE-75324 Uppsala | email: guy.lionel at gmail.com | mobile: +46 (0)73 9760618 | phone: +46 (0)18 410 7398


From guy.lionel at gmail.com  Mon Apr 13 20:31:45 2015
From: guy.lionel at gmail.com (Lionel Guy)
Date: Mon, 13 Apr 2015 20:31:45 +0200
Subject: [genoPlotR-help] Question about plot
In-Reply-To: <1428938766280352.974222773@ums005.ecc.u-tokyo.ac.jp>
References: <20150413150729.8B0FD18794D@r-forge.r-project.org>
 <F314A362-6007-4C8A-9FB7-6B8389B63636@gmail.com>
 <1428938766280352.974222773@ums005.ecc.u-tokyo.ac.jp>
Message-ID: <46AF102F-A5FE-4A18-AAE8-B72B45B90EC3@gmail.com>

A detailed explanation on the R graphical devices is beyond what I can provide as help, but have a look there:

https://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/Devices.html

You can open a pdf with 
pdf(file="myfile.pdf")
then do your plotting here. When you're done, close the graphical device with 
dev.off()

Cheers,

Lionel
> On 13 Apr 2015, at 17:26 , Zhu Bo <bozhu at ims.u-tokyo.ac.jp> wrote:
> 
> Hey Lionel,
>    Thanks for the quick response.. Well, I used exactly the same commands as 7.1.1. That means
> 
>> df1 <- data.frame(name = c("feat1", "feat2", "feat3"), start = c(2, 1000, 1050), end = c(600, 800, 1345), strand = c(-1, -1, 1), col = c("blue", "grey", "red"))
>> dna_seg1 <- dna_seg(df1)
>> df2 <- data.frame(name = c("feat1", "feat2", "feat3"), start = c(50, 800, 1200), end = c(900, 1100, 1322), strand = c(-1, 1, 1), col = c("blue", "grey", "red"))
>> dna_seg2 <- dna_seg(df2)
>> df3 <- data.frame(name = c("feat1", "feat2", "feat3"), start = c(1899, 2108, 2803), end = c(2034, 2732, 3620), strand = c(-1, -1, 1), col = rep("blue", 3))
>> dna_seg3 <- dna_seg(df3)
>> dna_segs <- list(dna_seg1, dna_seg2, dna_seg3)
>> plot_gene_map(dna_segs = dna_segs)
> 
> I just want to see how it works and then changed to my own data... Any idea how to export to a pdf or something? Coz I am using a server maybe difficult for me to connect a screen... Thanks
> 
> Best
> Bo Zhu
> ----- Original Message -----
>>> From: Lionel Guy <guy.lionel at gmail.com>
>>> To: Bo Zhu <bozhu at ims.u-tokyo.ac.jp>
>>> Cc: Help for genoPlotR <genoplotr-help at lists.r-forge.r-project.org>
>>> Date: 2015-04-14 00:20:18
>>> Subject: Re: Question about plot
>>> 
>>> Hi Bo Zhu,
>>> 
>>> Could you please give me the exact commands you input and the output of the program? 
>>> plot_gene_map() doesn't "print" anything, but opens a new window or outputs to the latest graphical device if any is open...
>>> 
>>> Cheers,
>>> 
>>> Lionel
>>> 
>>>> On 13 Apr 2015, at 17:07 , Bo Zhu <bozhu at ims.u-tokyo.ac.jp> wrote:
>>>> 
>>>> Hey Guys,
>>>>   I have one question about this software. I just start to learn this software and find it is pretty awesome. One problem, I don't need comparison function, gene structure and strand is enough for me. In this case, I tried to type the example 7.1.1 to learn. After the dna_segs <- list(dna_seg1, dna_seg2, dna_seg3) and I direct to print out by using 
>>>> plot_gene_map(dna_segs = dna_segs). But I found nothing print out. Could you please tell me what's wrong here and please let me know how to solve this problem. Thanks
>>>> 
>>>> Best
>>>> Bo Zhu
>>> 
>>> --
>>> Lionel Guy 
>>> F?lhagsleden 13, SE-75324 Uppsala | email: guy.lionel at gmail.com | mobile: +46 (0)73 9760618 | phone: +46 (0)18 410 7398
>>> 
>>> 

--
Lionel Guy 
F?lhagsleden 13, SE-75324 Uppsala | email: guy.lionel at gmail.com | mobile: +46 (0)73 9760618 | phone: +46 (0)18 410 7398