[R] find points on a graph

[David L Carlson]

You did not provide reproducible data since you didn't give us the "test"
file or any values for gene4 and gene5. You should read the posting
guideline (particularly the use of dput) and the documentation for package
ca.

I'm assuming that you want to plot supplementary rows (as described in the
ca documentation). Using your values, making some up for gene4 and gene5,
and combining them with the original data, you want the following:

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)))

This uses the first 3 rows for the correspondence analysis and then plots
rows 4 and 5 in that space using an open circle.

----------------------------------------------
David L Carlson
Associate Professor of Anthropology
Texas A&M University
College Station, TX 77843-4352


> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of aoife
> Sent: Wednesday, March 07, 2012 6:03 AM
> To: r-help at r-project.org
> Subject: Re: [R] find points on a graph
> 
> Many thanks for your reply.
> 
> Yes absolutely. So this is a small example:
> 
> > library(ca)
> > table <- read.table("test", header=TRUE)
> > table
>       codon1 codon2 codon3
> gene1    4.0      7     11
> gene2    7.0    222      8
> gene3    0.2      3      8
> > ca_analysis <- ca(table)
> > plot <- plot(ca_analysis)
> 
> and then i took a screen shot of the plot i can see.
> 
> http://r.789695.n4.nabble.com/file/n4453046/Screen_shot_2012-03-
> 07_at_12.00.44.png
> 
> so now for example i have a seperate file with 2 gene names:
> gene2
> gene3
> 
> and i want to find these two genes/nodes on the graph, and either
> highlight
> them a different color, or draw a border/shade them in some way.
> basically
> highlight them in any way?
> 
> is this any more helpful to explain what i mean?
> 
> Aoife
> 
> 
> 
> --
> View this message in context: http://r.789695.n4.nabble.com/find-
> points-on-a-graph-tp4452746p4453046.html
> Sent from the R help mailing list archive at Nabble.com.
> 
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> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.