R help - Jul 2006 - R newbie

Hello,

I am new to R and still feeling my way thru it. 

I am trying to plot the values from this file below on the X-axis of a plot. I
have attached the graph to the email...the one i am trying to recreate.

Exon	start		end
5'UTR	22540060	22540121
1	22540122	22540140
2	22540303	22540493
3	22541552	22541565
4	22542373	22542519
5	22544265	22544432
3'UTR	22544433	22544856


I would like to create small rectangles on the x-axis as colored boxes from
start position to end position of each exon...with the label showing 1, 2 etc
under each respective exon.

The 5' and 3' UTR would be colored different from the exons 1-5.


Any suggestions and ideas would greatly appreciated.

Thank you
Kiran


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Does this do what you want:


x <- "Exon    start           end
5'UTR   22540060        22540121
1       22540122        22540140
2       22540303        22540493
3       22541552        22541565
4       22542373        22542519
5       22544265        22544432
3'UTR   22544433        22544856"

y <- read.table(textConnection(x), quote='', header=TRUE)

# create the plot area
plot(range(y$start, y$end), c(1,7), type='n', xaxt='n',
yaxt='n',
    ylab='', xlab='')

# create the colored rectangles
rect(y$start, 1, y$end, 2, col=c('red', rep('green', nrow(y)-2),
'red'))

# put labels at midpoints of rectangles
axis(1, at=(y$start + y$end)/2, labels=as.character(y$Exon))



On 7/10/06, kannaiah@bsd.uchicago.edu <kannaiah@bsd.uchicago.edu>
wrote:
>
> Hello,
>
> I am new to R and still feeling my way thru it.
>
> I am trying to plot the values from this file below on the X-axis of a
> plot. I
> have attached the graph to the email...the one i am trying to recreate.
>
> Exon    start           end
> 5'UTR   22540060        22540121
> 1       22540122        22540140
> 2       22540303        22540493
> 3       22541552        22541565
> 4       22542373        22542519
> 5       22544265        22544432
> 3'UTR   22544433        22544856
>
>
> I would like to create small rectangles on the x-axis as colored boxes
> from
> start position to end position of each exon...with the label showing 1, 2
> etc
> under each respective exon.
>
> The 5' and 3' UTR would be colored different from the exons 1-5.
>
>
> Any suggestions and ideas would greatly appreciated.
>
> Thank you
> Kiran
>
>
> -------------------------------------------------
> This email is intended only for the use of the individual or entity to
> which
> it is addressed and may contain information that is privileged and
> confidential.  If the reader of this email message is not the intended
> recipient, you are hereby notified that any dissemination, distribution,
> or
> copying of this communication is prohibited.  If you have received this
> email
> in error, please notify the sender and destroy/delete all copies of the
> transmittal.  Thank you.
> -------------------------------------------------
>
>
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
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>

-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390 (Cell)
+1 513 247 0281 (Home)

What is the problem you are trying to solve?

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