[R] questions related to ploting in R

[Adaikalavan Ramasamy]

You have to decided whether you want one single plot or 23 plots (one
for each chromosome). Since I suspect that, say, copy_num at the end of
Chromosome 1 and the copy_num at the start of Chromosome 2 are not
related (like time series data) and would suggest 23 plots instead.


# simulate data #
df <- data.frame( Chromosome=rep(1:23, each=10), 
                  location=round(runif(230, max=1000000)), 
                  copy_num=runif(230, max=10) )

head(df)
  Chromosome location  copy_num
1          1   289588 7.3537879
2          1   267081 8.3605345
3          1   926470 0.1270541
4          1   214679 7.1798719
5          1   388366 4.2847290
6          1   332667 7.7888741
...

library(lattice)
xyplot( copy_num ~ location | Chromosome, data=df )


If you want it as one big plot, then you will need to somehow adjust the
location variable. I would suggest you think about putting the
chromosomes end to end. If you add the cumulative length of each
chromosome to the location to all the variables within a chromosome,
then you will get unique mapping for location. 

For example, if Chromosome 1 was 1,000,000 bases long and Chromosome 2
was 800,000 bases long, then a gene in location 500 of Chromosome 3
would actually be in position 1,800,500 (= 1,000,000 + 800,000 + 500) in
the overall map. Then you can simple plot the copy_num vs the new
location variable.

You might want to also check BioConductor packages if they have anything
more specific to your needs.

Regards, Adai



On Fri, 2004-08-06 at 16:03 -0400, Li, Aiguo (NIH/NCI) wrote:
> Dear all.
>  
> I need to draw a scatter plot of 23 chromosome copy numbers (y axes) against
> chromosome and physical location within each chromosome in one plot.  The
> data matrix looks as below:
>  
> chr  location copy_num
>  1   118345 1.320118
>  1   3776202 1.133879
>  1   4798845 0.989997
>  1   5350951 1.100967
> . more data here
> .
> .
>  2    118345 2.459119
>  2    157739 1.915919
>  2   1530065 1.924372
>  2   1530235 3.138177
> .
> .
> .
> more data here
> 23   118345     2.454111
> 23   5142838 1.719263
> 23   5163858 1.228840
>  
> The x axes of the plot should have chromosome label from 1 to 23 and
> physical location within each chromosome label.  The physical location
> values start from each chromosome (not necessaryly same value).  That means
> that x axes will have label (tick) for chromosome 1, within chromosome 1
> there are physical location from whatever value to the largest physical
> location value for chromosome 1, then chromosome 2 label, within chromosome
> 2 label physical location increase from whatever value to the largest
> physical location value for chromosome 2...... till chromosome 23.  
>  
> Is it possible to draw this type of plot in R? and How to draw it?
>  
> Thanks in advance
>  
> Aiguo Li, Ph.D.
> Bioinformatician & Molecular biologist
> NCI/NIH
>  
> 
> 
> 
> 
> 
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