[R] Fwd: Re: conditional coloring of image labels

From: Jake Michaelson <jjmichael_at_cc.usu.edu>
Date: Sat 12 Nov 2005 - 07:17:19 EST

Subject: Re: [R] conditional coloring of image labels Date: Friday 11 November 2005 1:04 pm
From: jim holtman <jholtman@gmail.com>
To: Jake Michaelson <jjmichael@cc.usu.edu>

Use 'mtext':

genes=cbind(ABC1=c(3,4,4,5,6,3), ABC2=c(4,3,4,7,7,8), ABC3=c(8,7,8,6,3,2)) ###plot the image
image(1:nrow(genes), 1:ncol(genes), genes, axes = FALSE, xlab = "", ylab = "", col=cm.colors(256))

sig=cbind(name=c("ABC1", "ABC2", "ABC3"), pvalue=c(0.005, 0.1, 0.001))

###label the axes
axis(1, 1:nrow(genes), labels = rownames(genes), las = 2, line = -0.5, tick =
0)

mtext(colnames(genes), side=2, las = 2, line = 1, at=1:3, col=ifelse(sig[, 'pvalue'] == '0.1', 'red', 'black'))

 On 11/11/05, Jake Michaelson <jjmichael@cc.usu.edu> wrote:
> On Friday 11 November 2005 10:37 am, Jake Michaelson wrote:
>
> I'll clarify a little and hopefully this will make more sense (thanks for
> the
> friendly encouragement):
>
> Let's say I have 6 samples and am looking at 3 genes, with intensities in
> a
>
> matrix as follows:
> > genes=cbind(ABC1=c(3,4,4,5,6,3), ABC2=c(4,3,4,7,7,8),
>
> ABC3=c(8,7,8,6,3,2))
>
> > genes
>
> ABC1 ABC2 ABC3
> [1,] 3 4 8
> [2,] 4 3 7
> [3,] 4 4 8
> [4,] 5 7 6
> [5,] 6 7 3
> [6,] 3 8 2
>
> ###plot the image
>
> >image(1:nrow(genes), 1:ncol(genes), genes, axes = FALSE, xlab = "", ylab
>
> =
> "", col=cm.colors(256))
>
> ###label the axes
>
> >axis(1, 1:nrow(genes), labels = rownames(genes), las = 2, line = -0.5,
>
> tick =
> 0)
>
> >axis(2, 1:ncol(genes), labels = colnames(genes), las = 2, line = -0.5,
>
> tick =
> 0)
>
> Now let's say (I'm just making these numbers and the scenario up here --
> for
> simplicity's sake) that I had run a statistical analysis previously and
> wanted to label the genes that showed a significance of p< 0.05. Let's say
> that ABC1 and ABC3 had p<0.05 (assume that these values would be in a
> two-column matrix with the gene name and its p-value).
>
> > sig=cbind(name=c("ABC1", "ABC2", "ABC3"), pvalue=c(0.005, 0.1, 0.001))
> > sig
>
> name pvalue
> [1,] "ABC1" "0.005"
> [2,] "ABC2" "0.1"
> [3,] "ABC3" "0.001"
>
> I now want these (the names of the significant genes) to be labeled in red
> rather than black on the plot. I would eventually write a script that
> would
> generate a large number of these images, each with a different set of
> genes.
> I would like to insert some sort of conditional formatting so that if that
> gene meets the significance threshold, the name is automatically plotted
> in
> red on the plot.
>
> I hope this is more clear and effective in explaining what I'm looking
> for.
>
>
> Thanks,
>
> --Jake
>
> > Hi all,
> >
> > I am interested in plotting a heatmap of a set of genes. I would like
>
> the
>
> > text labels of these genes to be colored red rather than black if they
>
> meet
>
> > certain statistical criteria (using an if statement). I'm not sure how
>
> to
>
> > change individual color labels without changing them all. Can anyone
> > provide some insight on how to do this?
> >
> > Thanks in advance,
> >
> > Jake
> >
> > ______________________________________________
> > R-help@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide!
> > http://www.R-project.org/posting-guide.html

--
Jim Holtman
Cincinnati, OH
+1 513 247 0281

What the problem you are trying to solve?

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Received on Sat Nov 12 07:23:50 2005

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