Dear Lists: I had a matrix which has lrt score for my microarray data. I just wonder how to visualize them with score over 20 in particular color such as blue. I cannot understand the color relationship with the value in z matrix. For example, If I see a red color in my image generated by image function. I don't know what is the value of z in that spot. Example: aaa <- matrix(rnorm(36),4,9) image(aaa) Can I paint the cells at which their values are higher than a certain value in image()? Or I have to use some other functions, best Shiliang [[alternative HTML version deleted]]
Joern Toedling
2007-Jul-25 21:14 UTC
[R] [BioC] Color Question about image function in graphics package
Hello Shiliang,
please have a look a the manual page for image (access from R by typing
"?image" ). You can specify which colors to use and at which values to
switch colors using the arguments breaks and colors. For example:
image(matrix(rnorm(36),4,9)+20,col=c("red","blue"),breaks=c(-1e5,20,1e5))
basically says: display every cell with a value below 20 in red
(breaks[1:2] specify the interval for "red") and every value above 20
in
blue
(breaks[2:3] specify the interval for "blue").
Regards,
Joern
swang wrote:> Dear Lists:
>
> I had a matrix which has lrt score for my microarray data. I just wonder
> how to visualize them with score over 20 in particular color such as blue.
> I cannot understand the color relationship with the value in z matrix. For
> example, If I see a red color in my image generated by image function. I
> don't know what is the value of z in that spot.
> Example:
> aaa <- matrix(rnorm(36),4,9)
> image(aaa)
>
> Can I paint the cells at which their values are higher than a certain value
> in image()?
> Or I have to use some other functions,
>
> best
>
> Shiliang
>
> [[alternative HTML version deleted]]
>
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