[BioC] Colouring limma MA plot

[Gordon K Smyth]

Dear Adam,

Why not simply use the 'values' and 'col' arguments to plotMA(), as 
described on the help page for plotMA?

Best wishes
Gordon

> Date: Mon, 12 Apr 2010 15:19:35 +0100
> From: adam_pgsql <adam_pgsql at witneyweb.org>
> To: BioConductor List <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] Colouring limma MA plot
>
>
> I am trying to colour a limma generated MA plot by fold change. I can do 
> it this way:
>
> status <- bugs.colour(RG,1)
> attr(status,"values") <- c("nonsignificant", "present", "absent", "Blank", "Buffer", "ACTB", "GAPDH", "Positive")
> attr(status,"col") <- c("black", "red", "green", "black", "brown", "pink", "yellow", "orange", "grey")
> plotMA(RG, array=1, status=status)
>
> bugs.colour <- function(RG, array) {
>    status <- RG$genes$Status
>
>    for (i in 1:length(status)) {
>        if (status[i] == "gene") {
>            if (is.na(RG$other$LogRatio[i,array])) {
>                status[i] = "nonsignificant"
>            }
>            else if (RG$other$LogRatio[i,array] > 0) {
>                status[i] = "present"
>            }
>            else { status[i] = "absent" }
>        }
>    }
>    status
> }
>
> but this seems to be a bit of a hack has i have hijacked the control 
> status... my question is, is there a better more efficient way to do 
> this?
>
> thanks
>
> adam

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