[R] plot question
Eric Thompson
ericthompso at gmail.com
Tue Oct 2 21:14:11 CEST 2007
But you did not use the command I suggested: you replaced x with
colnames(n), which is a vector of characters. Characters such as "25p"
has little meaning for plotting:
> as.numeric("25p")
[1] NA
So you've tried to plot a bunch of NA's, which is why it doesn't know
what limits to use for xlim.
That is why I gave you the commands to convert that character array
colnames(n) to a meaningful numeric array. It is unreasonable to
expect R to guess that "25p" = 25.
x <- colnames(n)
x <- as.numeric(substr(x, 1, nchar(x) - 1))
matplot(x, t(n), pch = 1, axes = FALSE)
axis(side = 2)
axis(side = 3, at = x, lab = colnames(n))
box()
On 10/2/07, Tiandao Li <Tiandao.Li at usm.edu> wrote:
> However, I got the following msg.
>
> > matplot(colnames(n), t(n), pch = 1, axes = FALSE)
> Error in plot.window(xlim, ylim, log, asp, ...) :
> need finite 'xlim' values
> In addition: Warning messages:
> 1: NAs introduced by coercion in: as.double.default(x)
> 2: no non-missing arguments to min; returning Inf in: min(x)
> 3: no non-missing arguments to max; returning -Inf in: max(x)
> 4: NAs introduced by coercion in: as.double.default(x)
>
>
>
> On Tue, 2 Oct 2007, Eric Thompson wrote:
>
> Okay. If you want to customize the axis labels, you can suppress the
> defaults by changing the matplot call to
>
> matplot(x, t(n), pch = 1, axes = FALSE)
>
> And then adding them how you want:
>
> axis(side = 2)
> axis(side = 3, at = x, lab = colnames(n))
> box()
>
>
>
> On 10/2/07, Tiandao Li <Tiandao.Li at usm.edu> wrote:
> > 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
> > >
> > > ______________________________________________
> > > R-help at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
> >
> > ______________________________________________
> > R-help at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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