[R] find points on a graph

[aoife]

Thank you. I really appreciate the help.

May i ask two questions.

In the example below:

table <- structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11,
    8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c("gene1",
    "gene2", "gene3", "gene4", "gene5"), c("codon1", "codon2",
    "codon3")))
Library(ca)
plot(ca(table, suprow=c(4, 5))) 

i get an output plot like this:

http://r.789695.n4.nabble.com/file/n4456264/Screen_shot_2012-03-08_at_12.16.41.png 

is it possible to add in code somewhere so that the nodes of interest are
not open circles, but are encompassed by a  shading on them, similar to
this:

http://r.789695.n4.nabble.com/file/n4456264/Screen_shot_2012-03-08_at_12.18.34.png 


And my second question, in this line of the code here:
plot(ca(table, suprow=c(4, 5))) 

is it possible to edit "suprow=c(4, 5)" to say "suprow=c(the genes that are
in a certain file)", i.e rather than manually type each gene in, get the
code to read in a file?

When i try move "gene 4" and "gene 5" to a seperate file, and try to read it
in, i get:

> plot <- ca(table,suprow=c(file))
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 
  'x' must be atomic

Many thanks for your time.

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