From: khush ........ <bioinfo.khush_at_gmail.com>

Date: Wed, 23 Jun 2010 10:02:49 +0530

R-help_at_r-project.org mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Wed 23 Jun 2010 - 04:35:57 GMT

Date: Wed, 23 Jun 2010 10:02:49 +0530

Hej Gregory,

Thanks for your reply and sorry for late reply, actually I was busy with
some other stuff but It helped me alot.

Thanks again sir.

Thanks to both of you.

Thank you

Jeet

On Wed, Jun 16, 2010 at 2:27 AM, Greg Snow <Greg.Snow_at_imail.org> wrote:

*> OK, I did not see the website before, here is some code to replicate the
**> example shown there (except I don’t do 3D effects):
**>
**>
**>
**> library(TeachingDemos)
**>
**>
**>
**> plot( c(1,1000), c(1,5), type='n', xlab='', ylab='', yaxt='n',
**> ylim=c(0.5,5.5) )
**>
**>
**>
**> tmpfun <- function( n, col, txt, cex=.5 ) {
**>
**> plot.window( c(-1,1), c(-1,1) )
**>
**> ms.filled.polygon( n=n, fg=col, bg=col, adj=0 )
**>
**> shadowtext(0,0, txt, cex=cex)
**>
**> }
**>
**>
**>
**> lines( c(1,700), c(1,1), col='grey', lwd=3 )
**>
**>
**>
**> lines( c(100,100,200,200), c(1,1.25,1.25,1) )
**>
**>
**>
**> lines( c(320,320), c(1,1.25), col='red' )
**>
**> points( 320, 1.25, pch=18, col='red' )
**>
**>
**>
**> subplot( tmpfun(400, 'grey15', 'MY'), c(50, 150), c(0.85,1.15) )
**>
**> subplot( tmpfun(5, 'green', 'DOM'), c(300, 400), c(0.85, 1.15) )
**>
**>
**>
**>
**>
**> Hope this helps get you started (this could all be wrapped into a single
**> function if you want, additional proteins can be added at 2, 3, …),
**>
**>
**>
**> --
**>
*

> Gregory (Greg) L. Snow Ph.D.

*>
**> Statistical Data Center
**>
**> Intermountain Healthcare
**>
**> greg.snow_at_imail.org
**>
**> 801.408.8111
**>
**>
**>
**> *From:* khush ........ [mailto:bioinfo.khush_at_gmail.com]
**> *Sent:* Monday, June 14, 2010 11:21 PM
**> *To:* Greg Snow
**> *Cc:* Petr PIKAL
**>
**> *Subject:* Re: [R] points marking
**>
**>
**>
**> Dear Gregory ,
**>
**> Thanks for your kind reply, and consideration towards my query, well have
**> you check with the link that I sent you the other day (
**> http://www.expasy.ch/tools/mydomains/), in which you need to set the
**> protein length first and then the domain data, with various shapes i.e 1-6
**> and 4 different colors respectively.
**>
**> In the second part of the example,
**>
**> 50 ,150 , 2,4, MY
**> 300 ,400 , 3,2, DOM
**>
**> I am drawing all the data with barplots as they are so many so I am using
**> barplots, and they are of variuos length, as I mentioned in Dom (has all the
**> protein lengths in it), now I wanted to draw various shapes to my data say
**> on bar 1 of barplots segments 50-150 has shapes say x and color = red, adn
**> its name is MY , and this could repeat for other bars of the plot but with
**> different points .
**>
**> same like other if I want to plot the segments 300-400 with shapes say y
**> and color = red and its name should be DOM
**>
**> I want to make a script which could take the length of the protein and draw
**> corresponding domains on it. Hope you understand the way I am explaining you
**> now. Please feel free to ask further if needed.
**>
**>
**> Thank you
**> Jeet
**>
**>
**> On Mon, Jun 14, 2010 at 9:13 PM, Greg Snow <Greg.Snow_at_imail.org> wrote:
**>
**> I don’t think that I would use a barplot as the base, but rather just set
**> up the graph and add the lines where I wanted them. I still don’t
**> understand what you want your graph to look like, or what question you are
**> trying to answer with it (part may be a language barrier). If you can give
**> us a better example of what you are trying to accomplish, or a better
**> description of what your data is like and what you are trying to get from
**> the graph, we will have a better chance of being able to help you.
**>
**>
**>
**> --
**>
**> Gregory (Greg) L. Snow Ph.D.
**>
**> Statistical Data Center
**>
**> Intermountain Healthcare
**>
**> greg.snow_at_imail.org
**>
**> 801.408.8111
**>
**>
**>
**> *From:* khush ........ [mailto:bioinfo.khush_at_gmail.com]
**> *Sent:* Saturday, June 12, 2010 5:38 AM
**> *To:* Greg Snow
**> *Cc:* r-help_at_r-project.org; Petr PIKAL
**>
**>
**> *Subject:* Re: [R] points marking
**>
**>
**>
**> Hi,
**>
**> Well Thanks for letting me know that pch is of no use with segments petr. I
**> am using lend as it suits to me more as gregory suggested , but I am not
**> getting imite??? think I try to fix it with some other method also, as I
**> have to deal more with the symbols in this case, But I want to the know one
**> thing from you guys that the way I am using the code is good enough to
**> start, as I am not much familiar with this suff or its dirty way to handle
**> such task. please let me know.
**>
**> Thanks gregory and petr.
**>
**> Thank you
**> Jeet
**>
**>
**>
**> On Fri, Jun 11, 2010 at 9:07 PM, Greg Snow <Greg.Snow_at_imail.org> wrote:
**>
**> Those graphs look like chromosome maps, if so, you may want to look into
**> the bioconductor project, they may have some prewritten functions to do
**> this. If not, the lend argument (see ?par) may be something to look at. If
**> you really want points and segments you will need to plot the points with
**> the points function and the segments separately. Segments can take vectors,
**> so you don’t need to separate things into multiple calls.
**>
**>
**>
**> --
**>
**> Gregory (Greg) L. Snow Ph.D.
**>
**> Statistical Data Center
**>
**> Intermountain Healthcare
**>
**> greg.snow_at_imail.org
**>
**> 801.408.8111
**>
**>
**>
**> *From:* khush ........ [mailto:bioinfo.khush_at_gmail.com]
**> *Sent:* Friday, June 11, 2010 12:00 AM
**> *To:* Greg Snow
**> *Cc:* r-help_at_r-project.org
**> *Subject:* Re: [R] points marking
**>
**>
**>
**> Dear Gregory ,
**>
**> Thnaks for your reply and help. I am explaining you my problems again,
**> below is my script for the same .
**>
**> Dom <-c (195,568,559)
**>
**> fkbp <- barplot (Dom, col="black", xlab="", border = NA, space = 7,
**> xlim=c(0,650), ylim =c(0, 87), las = 2, horiz = TRUE)
**>
**> axis (1, at = seq(0,600,10), las =2)
**>
**> 1. ==============Segments 1=================================
**>
**> segments(164,7.8,192,7.8, col = "green", pch=23, cex="9", lty="solid",
**> lwd=20)
**> segments(45,15.8,138,15.8, col = "green", pch=23, cex="9", lty="solid",
**> lwd=20)
**> segments(160,15.8,255,15.8, col = "green", pch=23, cex="9", lty="solid",
**> lwd=20)
**> segments(277,15.8,378,15.8, col = "green", pch=23, cex="9", lty="solid",
**> lwd=20)
**> segments(51,23.8,145,23.8, col = "green", pch=23, cex="9", lty="solid",
**> lwd=20)
**> segments(167,23.8,262,23.8, col = "green", pch=23, cex="9", lty="solid",
**> lwd=20)
**> segments(284,23.8,381,23.8, col = "green", pch=23, cex="9", lty="solid",
**> lwd=20)
**>
**> 2. ==============Segments 2 ==================================
**> segments(399,15.8,432,15.8, col = "blue", pch=21, cex="9", lty="solid",
**> lwd=20)
**> segments(448,15.8,475,15.8, col = "blue", pch=21, cex="9", lty="solid",
**> lwd=20)
**> segments(486,15.8,515,15.8, col = "blue", pch=21, cex="9", lty="solid",
**> lwd=20)
**> segments(401,23.8,434,23.8, col = "blue", pch=21, cex="9", lty="solid",
**> lwd=20)
**> segments(450,23.8,475,23.8, col = "blue", pch=21, cex="9", lty="solid",
**> lwd=20)
**> segments(486,23.8,517,23.8, col = "blue", pch=21, cex="9", lty="solid",
**> lwd=20)
**>
**> I solved one part of my query i.e to mark points from one positions to
**> other is ok and I found that its working fine but I have another issue now,
**> as I am using using two segments data 1 and 2 , although I want to draw
**> different shapes for segmants 2 as I am giving pch=21, but I it seems to
**> give a solid line for both. I want to draw different shapes for every chunk
**> of segments i.e is the whole point.
**>
**> I want to make script which can generate such figures, below is link to one
**> of the tool.
**> http://www.expasy.ch/tools/mydomains/
**>
**> Thank you
**>
**> Jeet
**>
**> On Thu, Jun 10, 2010 at 11:10 PM, Greg Snow <Greg.Snow_at_imail.org> wrote:
**>
**> Your question is not really clear, do either of these examples do what you
**> want?
**>
**> with(anscombe, plot(x1, y2, ylim=range(y2,y3)) )
**> with(anscombe, points(x1, y3, col='blue', pch=2) )
**> with(anscombe, segments(x1, y2, x1, y3, col=ifelse( y2>y3, 'green','red')
**> ) )
**>
**>
**> with(anscombe, plot(x1, y2, ylim=range(y2,y3), type='n') )
**> with(anscombe[order(anscombe$x1),], polygon( c( x1,rev(x1) ), c(y2,
**> rev(y3)), col='grey' ) )
**>
**>
**>
**> --
**> Gregory (Greg) L. Snow Ph.D.
**> Statistical Data Center
**> Intermountain Healthcare
**> greg.snow_at_imail.org
**> 801.408.8111
**>
**>
**>
**> > -----Original Message-----
**> > From: r-help-bounces_at_r-project.org [mailto:r-help-bounces_at_r-
**> > project.org] On Behalf Of khush ........
**> > Sent: Thursday, June 10, 2010 7:48 AM
**> > To: r-help_at_r-project.org
**> > Subject: [R] points marking
**> >
**> > Hi,
**> >
**> > How to mark points on x axis of a graph keeping x axis as constant and
**> > changing y from y1 to y2 respectively. I want to highlight the area
**> > from y1
**> > to y2.
**> >
**> > Any suggestions
**> >
**> > Thank you
**> > Jeet
**> >
**>
**> > [[alternative HTML version deleted]]
**> >
**> > ______________________________________________
**> > R-help_at_r-project.org mailing list
**> > https://stat.ethz.ch/mailman/listinfo/r-help
**> > PLEASE do read the posting guide http://www.R-project.org/posting-
**> > guide.html
**> > and provide commented, minimal, self-contained, reproducible code.
**>
**>
**>
**>
**>
**>
**>
*

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