Re: [R] conditional coloring of image labels

From: Jake Michaelson <jjmichael_at_cc.usu.edu>
Date: Sat 12 Nov 2005 - 06:36:44 EST

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
>
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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 Received on Sat Nov 12 06:47:31 2005

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