[R] plot question

[Tiandao Li]

Thanks for your quick reply, Eric.

I want plot colnames(n) as string on x-axis. If the regression lines don't 
fit the data very well, it is OK, the plot is only for quality check.


On Tue, 2 Oct 2007, Eric Thompson wrote:

If I've correctly interpreted what you want, you first need to get the x values:

x <- colnames(n)
x <- as.numeric(substr(x, 1, nchar(x) - 1))

Then it seems fairly easy to use matplot to get the values with
different colors for each concentration

dim(x) <- c(length(x), 1)
matplot(x, t(n), pch = 1)

But this does not look like a simple line will fit the data for each
gene well, so perhaps I've misunderstood something. You will have to
decide how you want to do the regression. It will also get very messy
and difficult to read with 20 lines (a different regression for each
gene). To do the regressions, plot the lines, and label with the gene
ID, see

?lm
?predict
?abline
?text




On 10/2/07, Tiandao Li <Tiandao.Li at usm.edu> wrote:
> Hello,
>
> I have a question about how to plot a series of data. The folloqing is my
> data matrix of n
> > n
>              25p    5p  2.5p 0.5p
> 16B-E06.g 45379  4383  5123   45
> 16B-E06.g 45138  4028  6249   52
> 16B-E06.g 48457  4267  5470   54
> 16B-E06.g 47740  4676  6769   48
> 37B-B02.g 42860  6152 19276   72
> 35B-A02.g 48325 12863 38274  143
> 35B-A02.g 48410 12806 39013  175
> 35B-A02.g 48417  9057 40923  176
> 35B-A02.g 51403 13865 43338  161
> 45B-C12.g 50939  3656  5783   43
> 45B-C12.g 52356  5524  6041   55
> 45B-C12.g 49338  5141  5266   41
> 45B-C12.g 51567  3915  5677   43
> 35A-G04.g 40365  5513  6971   32
> 35B-D01.g 54217 12607 13067   93
> 35B-D01.g 55283 11441 14964  101
> 35B-D01.g 55041  9626 14928   94
> 35B-D01.g 54058  9465 14912   88
> 35B-A04.g 42745 12080 34271  105
> 35B-A04.g 41055 12423 34874  126
>
> colnames(n) is concentrations, rownames(n) is gene IDs, and the rest is
> Intensity. I want to plot the data this way.
> x-axis is colnames(n) in the order of 0.5p, 2.5p,5p,and 25p.
> y-axis is Intensity
> Inside of plot is the points of intensity over 4 concentrations, points
> from different genes have different color or shape. A regression line of
> each genes crosss different concetrations, and at the end of line is gene
> IDs.
>
> Thanks,
>
> Tiandao
>
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