[R] plot question
Eric Thompson
ericthompso at gmail.com
Tue Oct 2 19:13:46 CEST 2007
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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