[Traminer-users] loop for plotting quality statistics from wcKMedRange

[thomas collas]

Sure, you can use the pdf() function before the par() one. As quartz(),
pdf() allows to define the dimensions of the window. Instead of par(), the
layout() function is great too to divide the window into several plots. The
pdf() file is produced while R meets the dev.off() line after the commands
generating the plots, the axes, and so on.

pdf(file="working_directory/plots.pdf", height=, etc.)

par(mfrow=c(1,2))

for (i in stats) {

  plot(i, stat=c("ASW","HC", "R2", "PBC", "HG"), legendpos="topright", norm=
"zscore")

 }
dev.off()

Best,
thomas

2016-10-08 14:09 GMT+02:00 Reynolds, Jeremy E <reyno113 at purdue.edu>:

> Thank you Thomas!  It is amazing how many things a novice user can mess up
> in just a few lines. Loops and the apply functions seem to be a perenniaI
> source of confusion in R.
>
> I was hoping to save the plots in a single file (perhaps PDF?).  Do you
> have any additional tips for that?
>
> Thanks
> Jeremy
>
> Sent from my iPhone
>
> On Oct 8, 2016, at 2:10 AM, thomas collas <thomas.collas at gmail.com> wrote:
>
> Dear Jeremy,
> That should work if you change 3 things :
> - the first problem is your stats object, which is a character vector, not
> a list of objects, you can't plot a character string.
> - the second problem is the "x" in the plot function. If i is a component
> and not an attribute of stats, you can't index stats with i.
> - the third smaller problem is that you have to ask R to print two plots.
> If it is only for visualization, you can use the mfrow argument in the
> par() function.
>
> After having created the two objects you want to plot, this code should
> work :
>
> stats <- list(pamomf2i5q.w, pamwardomf2i5q.w)
>
> par(mfrow=c(1,2))
>
> for (i in stats) {
>
>   plot(i, stat=c("ASW","HC", "R2", "PBC", "HG"), legendpos="topright",
> norm="zscore")
>
>  }
> Best,
> thomas
>
> 2016-10-08 4:41 GMT+02:00 Reynolds, Jeremy E <reyno113 at purdue.edu>:
>
>> Dear TraMineR Users,
>>
>>
>>
>> I would like to loop through many sets of clustering results produced
>> with wcKMedRange and produce a plot for each one.  Without the loop, the
>> code would look like this:
>>
>>
>>
>> plot(pamomf2i5q.w, stat=c("ASWw","HC", "R2", "PBC", "HG"),
>> legendpos="topright", norm="zscore")
>>
>> plot(pamwardomf2i5q.w, stat=c("ASWw","HC", "R2", "PBC", "HG"),
>> legendpos="topright", norm="zscore")
>>
>>
>>
>> When I try to put this in a loop, I get the error messages below
>> suggesting that R is expecting a y value in the plot command.  Is there
>> something wrong with my loop that is causing this problem?
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Jeremy
>>
>>
>>
>>
>>
>> > stats <- c("pamomf2i5q.w", "pamwardomf2i5q.w")
>>
>> > for (i in unique(stats)) {
>>
>> +   plot(stats[i], stat=c("ASW","HC", "R2", "PBC", "HG"),
>> legendpos="topright", norm="zscore")
>>
>> + }
>>
>> <image001.png> Show Traceback
>>
>>  Rerun with Debug
>>
>> Error in plot.window(...) : need finite 'ylim' values
>>
>> In addition: Warning messages:
>>
>> 1: In min(x) : no non-missing arguments to min; returning Inf
>>
>> 2: In max(x) : no non-missing arguments to max; returning -Inf
>>
>> 3: In plot.window(...) : "stat" is not a graphical parameter
>>
>> 4: In plot.window(...) : "legendpos" is not a graphical parameter
>>
>> 5: In plot.window(...) : "norm" is not a graphical parameter
>>
>>
>>
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>
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