[R-SIG-Mac] Problem with tkrplot and affylmGUI

[James Wettenhall]

[ CCing to Keith, who is taking over maintenance of limmaGUI and affylmGUI
from me]

Hi Bernard,

You can actually do without tkrplot.  I have had some problems with
tkrplot on MacOSX in the past, e.g. at one stage I couldn't find a working
binary of tkrplot on CRAN and I had trouble building it from source.  Down
the bottom of the Plot menu in limmaGUI or affylmGUI there is an "Options"
item, where you can choose between using tkrplot and using the standard R
graphics device (Quartz for Mac users).  On Mac, the default should be NOT
to use tkrplot, so my apologies for the confusion about tkrplot being
"required".

I can give you the reasons for using tkrplot (and for not using it), but
they are a bit long winded...

Most Windows users run R in MDI (Multiple Document Interface) mode, so
when running an R Tcl/Tk application like limmaGUI, many users minimize
the entire MDI frame, so then it makes sense for limmaGUI to plot in Tk
windows so that the plots are not hidden within the minimized MDI frame. 
A major disadvantage of using tkrplot is that you cannot resize plots by
dragging the corner of the window (although you can be entering numerical
horizontal and vertical scaling factors).  Probably the biggest advantage
of using tkrplot in limmaGUI is that there is at least one interactive
plot, the immage array plot.  One pixel is plotted for each spot (gene) on
a microarray slide colored between red and green depending on its log
ratio.  If you click on one pixel of this image, you can determine which
gene you are looking at (but this only works with tkrplot).  One thing to
note when using Quartz with limmaGUI, is that when you plot a new graph,
by default it will overwrite the current plot window, but you can open a
new Quartz window by activating the R application and then using the
Windows pulldown menu at the top of your screen.

So, perhaps tkrplot should be phased out (and the interactive stuff could
be implemented differently using the locator() function in R, but using
tkrplot is still the default for Windows users.

Hope this helps,
James

> Dear all,
>
> As affylmGUI requires tkrplot package from R, I have installed tkrplot
> package from CRAN and when I load the library for tkrplot, I get the
> following error:
>
>> library(tkrplot)
> Loading required package: tcltk
> Error in structure(.External("dotTcl", ..., PACKAGE = "tcltk"), class
> = "tclObj") :
> 	[tcl] no suitable image found.  Did find:
> 	/Library/Frameworks/R.framework/Versions/2.1.1/Resources/library/tkrplot/libs/tkrplot.so:
> not a dylib.
> Error in library(tkrplot) : .First.lib failed for 'tkrplot'
>
> On another note, it is related to the problem when I do the following:
>
>> library(affylmGUI)
>> affylmGUI()
>
> The affylmGUI program is loaded up but you will encounter the error box:
> Error in eval(expr, envir, enclos);
> Object "PlotOptions" not found
>
> The problems, I think that it's related as affylmGUI requires tkrplot
> package
>
> Does anyone have possible solutions?
>
> Cheers in advance in helping me to solve the problem.
>
> yours sincerely,
> Bernard
>
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