On 11/14/2012 11:04 AM, michele caseposta wrote:
Hi everyone,
I have a certain number of samples and I want to visualize the groups those
samples belong to.
For example, suppose to have three variables, age, sex, and smoker/nonsmoker,
and three samples, S1, S2, S3.
S1 is 35, male, nonsmoker
S2 is 24, female, nonsmoker
S3 is 24, female, smoker
at the end I have the following data frame:
S1 S2 S3
age 35 24 30
sex M F F
smk N N S
What I would like is to see this represented in a matrix with colors
representing the group the specific sample belongs to. In the example, Age
would have three levels, sex and smoker/nonsmoker will have two.
An example of what I would like to obtain is from the attached image (from The
Cancer Genome Browser at UCSC)
You can see the class of each sample represented by the color.
Clearly here there are useless variables, like sample name, but the example
gives an idea of what I would like to get.
So far I was able to achieve a pseudo-result with colorbar.plot, but I find it
hard to get the labels in the correct position, as it seems like I cannot find
a way to automatically put them near each class bar
Any suggestions other than colorbar.plot?
Hi michele,
Your picture didn't come thought, but it was fairly easy to find. I'm
not entirely sure about this, but are you looking for an hierarchic
breakdown of your variables? The illustration on the right side of your
example looks like this. Sizetrees provide such a breakdown by
successive stacked bars, in which each bar in the leftmost stack splits
into its components, like smoke -> sex -> age. Alternatively you can
illustrate relationships like these with nested bar plots, in which
subcategories are nested within the superordinate categories. See the
sizetree and barNest functions in the plotrix package.
Jim
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