Dear Jonathan,

Thanks a lot for your help! That works pretty well!

Best wishes,
Wei

On 7/15/10 5:52 PM, Jonathan Flowers wrote:
> Hi,
>
> What if you create two data frames, then merge them by gene id.
>
> If your data is in a data frame called "dframe"...
>
> df1 <- subset(dframe,select=c("id2c","2c"))
> df2 <- subset(dframe,select=c("id1c","1c"))
>
> merged <- merge(df1,df2,by.x="id2c",by.y="id1c",all=TRUE)
>
> plot(merged$1c,merged$2c)
>
> Cheers,
>
> Jonathan
>
>
> On Thu, Jul 15, 2010 at 5:12 AM, Yanwei Tan 
> <Tan@nbio.uni-heidelberg.de <mailto:Tan@nbio.uni-heidelberg.de>> wrote:
>
>     Dear all,
>
>     I would like to make a scatter plot using "plot" function.  I have two
>     sample 1c and 2c, the 1st and 3rd are the ID of each gene, the 2nd and
>     3rd are the values.  But as you can see some genes are not in the same
>     row, i.e: ENSMUSG00000001020 is in the 4th row in sample 2c and
>     7th row
>     of the sample 1c.  But I have nearly 1000 genes, I can not edit
>     the data
>     manually to fit the "plot" function.
>
>     Does "Plot" can automatically recognize every gene in different row of
>     samples? If I simply do "plot(2c,1c)", then I guess the dot about gene
>     ENSMUSG00000001020 would be (0.122112211, 0.655010678 ) instead of
>     (0.122112211, 0.15301479).
>
>     Can someone give me some hint?
>
>     With many thanks in advance!
>
>     Best wishes,
>     Wei
>
>
>     id2c    2c      id1c    1c
>     ENSMUSG00000000184      0.345889139     ENSMUSG00000000184    
>      0.601580659
>     ENSMUSG00000000202      0.310589755     ENSMUSG00000000202    
>      0.422453875
>     ENSMUSG00000000531      1.945122637     ENSMUSG00000000355    
>      0.633385261
>     ENSMUSG00000001020      0.122112211     ENSMUSG00000000567    
>      0.655010678
>     ENSMUSG00000001228      0.157001414     ENSMUSG00000000948    
>      0.785187729
>     ENSMUSG00000001403      0       ENSMUSG00000000957      0.643804965
>     ENSMUSG00000001435      1.865292034     ENSMUSG00000001020    
>      0.15301479
>     ENSMUSG00000001473      2.156209643     ENSMUSG00000001025    
>      0.43609215
>     ENSMUSG00000001508      3.736633663     ENSMUSG00000001228    
>      0.087437023
>     ENSMUSG00000001604      3.846534653     ENSMUSG00000001403    
>      0.045904437
>     ENSMUSG00000001655      NA      ENSMUSG00000001435      1.3497589
>     ENSMUSG00000001773      0.10990099      ENSMUSG00000001506    
>      0.688566553
>     ENSMUSG00000001864      0.212711594     ENSMUSG00000001555    
>      0.571640157
>     ENSMUSG00000002055      0.224287735     ENSMUSG00000002055    
>      0.393466602
>     ENSMUSG00000002076      13.18811881     ENSMUSG00000002076    
>      13.77133106
>     ENSMUSG00000002274      0.318134445     ENSMUSG00000002265    
>      0.659467911
>
>
>
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>
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>
>

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