[BioC] flowStats quadrantGate and 'names'

[Aric Gregson]

On Thu, 23 Sep 2010 14:48:38 -0700
Nishant Gopalakrishnan <ngopalak at fhcrc.org> wrote:

> I am not sure what 'names' function in flowViz you are talking about.
> I do not see one in flowViz. Its hard to guess what you have done
> without providing some reproducible lines of code.
> 
> With regard to putting in custom labels inside the plots. (if that’s
> what you are trying to do) FlowViz does not have a direct option of
> placing the the summary stats/custom text inside the plots.

I see that it appears to have been removed from flowViz. Previously, if
set 'names=TRUE', the name of the gated population (i.e., filterName)
would be printed on the plot near the gate outline. I had modified it
as below to include percentages of parent populations. Most flow
software does this automatically as an option. Here is an example that
I have used in published figures:

plot344livebw <-xyplot(`Indo.1..Violet..A` ~ `APC.H7.A`,
Data(wf[["logicle"]])[[6]],  
ylim=c(-1,11.75),
smooth=F,
alpha=0.5,
col="grey70",                     
scales=list(tick.number=6), 
aspect="iso",
filter=livefilter,
names="\n6.3%",
main="Live CD4 Gate\nSinglet+",
xlab = "CD4 APC-H7",
ylab = "UV Blue Live/Dead",
par.settings=list(gate=list(col="grey10", alpha=.5), 
    gate.text=list(col="black", alpha=0.3, cex=2)))
                   
So, it used to do something.
 
> However, if you are keen of placing some of the labels/summary stats
> that you need on the plot, it can be done but will require some extra
> effort.
> 
> 1. You will need to create a custom panel function that does what you
> need and pass this to the panel argument of the xyplot function in
> flowViz. 2. Please have a look at the panel.xyplot.flowFrame method
> in the flowViz package You will need to modify this to add your text
> label. You could add something like
> gltext(xposition, yposition, "your label",..., gp= gpar$gate.text)
> after the polygon is drawn to add a label at the position (xposition,
> yposition) on the plot.
> 3. Call xyplot with the panel argument set to the function that you
> just modified

I will give this a try...

Thanks, Aric