[BioC] Colouring limma MA plot

[Wolfgang Huber]

Hi Adam,

Efficiency: have a look at the "ifelse" function for vectorised 
if-functionality that allows you to avoid the for-loop in your 
'bugs.colour' function.

Goodness: I don't think you need to be worrying about hijacking the 
control status for your purpose, since it's the limma::plotMA function 
that hijacked plot's "col" argument in the first place. However, if this 
leads to serious trouble, the cleanest is probably to write your own 
function on top of graphics::plot (or lattice::xyplot), since the added 
functionality of limma::plotMA is not that complex.

	Best wishes
	Wolfgang


adam_pgsql scripsit 12/04/10 16:19:
> 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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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber